Asymmetric Unit (asymmetric + unit)

Distribution by Scientific Domains

Kinds of Asymmetric Unit

  • crystallographic asymmetric unit

  • Selected Abstracts

    Crystal structure of a tetrazole derivative

    H. S. Yathirajan
    Abstract 5-(4'-Methyl-1,1'-biphenyl-2-yl)-1H-tetrazole(MBT), C28H24N8, CCDC: 223082, F.W.=472.55, triclinic, P1, a=4.99(1)Å, b=14.25(4)Å, c=16.63(5)Å, , = 90.27(5)°, , = 91.19(5)°, , = 90.64(5)°, V = 1182(6)Å3, Z = 4, Dcal = 1.327 Mgm -3, , = 0.084mm -1, F000 = 496, , (MoK,) = 0.71073Å, final R1 and wR2 are 0.0924 and 0.2309, respectively. There are two crystallographically independent molecules in the asymmetric unit. The dihedral angles between the two phenyl rings of the biphenyl ring system are 44.2(2)° and 44.3(2)° for the two molecules respectively. The molecules are stabilized by N-H,N and C-H,N types of intermolecular hydrogen bonds in the unit cell in addition to van der Waals forces. © 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim [source]

    Crystal structures and spectroscopic characterization of chiral and racemic 4-phenyl-1,3-oxazolidin-2-one

    S. Kitoh
    Abstract Crystal structures of (R)- and (rac)-4-phenyl-1,3-oxazolidin-2-one (4-POO) have been determined by X-ray diffraction and characterized by the solid state 13C NMR and IR spectra. Molecular geometries and intermolecular interactions in (R)- and (rac)-4-POO crystals are very similar to each other; 4-POO molecules are linked via the N-H,O intermolecular hydrogen bonds to form the chained structure. Chemical shifts of the solid state 13C NMR spectra are very similar to each other, whereas the 1H spin-lattice relaxation times (T1H) value for (R)-4-POO is five times as large as that for (rac)-4-POO, reflecting the more restricted mobility of the (R)-4-POO chain. Although both crystals contain an unique molecule in the asymmetric unit, a doublet feature is observed for the C=O stretching mode in the IR spectra of (R)- and (rac)-4-POO crystals. The frequency gap of the C=O bands are correlated with the strength of the dipole-dipole interactions between the neighboring C=O groups. © 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim [source]

    Transition Metal-Assisted Hydrolysis of Pyrazole-Appended Organooxotin Carboxylates Accompanied by Ligand Transfer

    Vadapalli Chandrasekhar
    Abstract The reaction of the potentially multi-site coordination ligands [{nBu2SnO2CL}2O]2 (1), [{nBu2SnO2CL,}2O]2 (2), [nBuSn(O)O2CL]6 (3), and [nBuSn(O)O2CL,]6 (4), (L = (Pz)2CH-); L, = (3,5-Me2Pz)2CH-; Pz = pyrazolyl) with hydrated metal salts leads to the hydrolysis of the organotin carboxylates accompanied by the formation of insoluble organotinoxide/hydroxides and metal complexes. The in situ generated LCOO and L,COO ligands bind to the metal ions. The complexes [Cu(LCOO)2(NO3)2(nBu2Sn((H2O)2)]n[Cu(LCOO)2] (5), [Mg(L,COO)2] (6), [Cu(LCOO)2] (7), and [{(Cu(L,COO)2(Cu(MeOH))3}{ClO4}2]n (8) were isolated and structurally characterized. The solid-state structure of 5 reveals that two discrete molecules are present in the same asymmetric unit; a heterobimetallic coordination polymer, [Cu(LCOO)2(NO3)2(nBu2Sn((H2O)2)]n and a discrete coordination complex, [Cu(LCOO)2]. The cationic portion of the heterobimetallic compound contains alternate six-coordinate SnIV and CuII centers bridged by the carboxylate oxygen atoms of the LCOO ligand.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source]

    Efficient DNA Cleavage Induced by Copper(II) Complexes of Hydrolysis Derivatives of 2,4,6-Tri(2-pyridyl)-1,3,5-triazine in the Presence of Reducing Agents

    Joaquín Borrás
    Abstract The reaction of 2,4,6-tri(pyridyl)-1,3,5-triazine (ptz) and copper(II) salts in dmf/water (1:1) results in the hydrolysis of ptz and formation of the anions bis(2-pyridylcarbonyl)amide (ptO2,) and bis(2-pyridylamine)amide (ptN2,), which are found in the complexes [Cu(ptN2)(OAc)]·3H2O (1), [Cu(ptO2)(OAc)(H2O)]·H2O (2), [Cu(ptN2)(for)]·3H2O (3) (for = formate), [Cu(ptO2)(for)(H2O)] (4), [Cu(ptO2)(benz)]·H2O (5) (benz = benzoate), and [Cu(ptO2)F(H2O)]2·3H2O (6). This report includes the chemical and spectroscopic characterization of all these complexes along with the crystal structures of 4,6. The coordination spheres of CuII in 4 and 5 are best described as distorted tetragonal square pyramidal for the former and distorted square planar for the latter. The crystal structure of 6 shows the presence of two discrete monomeric [Cu(ptO2)F(H2O)] entities in the crystallographic asymmetric unit in which both copper(II) ions have a distorted square-pyramidal coordination geometry. The binding of the complexes to DNA has been investigated with the aid of viscosity and thermal denaturation studies, both of which indicate that the interaction is probably due to the outer-sphere mechanism. The ability of the compounds to cleave DNA has also been tested. Efficient oxidative cleavage was observed in the presence of a mild reducing agent (ascorbate) and dioxygen. Mechanistic studies with reactive oxygen species (ROS) scavengers confirm that hydrogen peroxide, the hydroxyl radical, singlet oxygen-like species, and the superoxide anion are necessary diffusible intermediates in the scission process. A mechanism involving either the Fenton or theHaber,Weiss reaction plus the formation of copper oxene species is proposed for the DNA cleavage mediated by these compounds.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source]

    Solvothermal Synthesis, Crystal Structures, and Properties of New Selenidoantimonates [Ln(en)4(SbSe4)] (Ln = La, Nd) and [Sm(en)4]SbSe4·0.5en: The First Example of an SbSe43, Anion Acting as a Ligand to a Lanthanide Complex

    Ding-Xian Jia
    Abstract Three new lanthanide selenidoantimonates [Ln(en)4(SbSe4)] [Ln = La (1), Nd (2)] and [Sm(en)4]SbSe4·0.5en (3) (en = ethylenediamine) were first synthesized by treating LnCl3, Sb, and Se in a stoichiometric ratio with en under mild solvothermal conditions. Compounds 1 and 2 are isostructural. The Ln3+ ion has a nine-coordinate environment involving eight N atoms from four en ligands and one Se atom from the SbSe43, anion forming a distorted bicapped pentagonal bipyramid. [La(en)4(SbSe4)] and [Nd(en)4(SbSe4)] are the first examples of solvothermally synthesized selenidoantimonates with an SbSe43, anion acting as a ligand in a lanthanide complex. The crystal structure of 3 contains an isolated bicapped trigonal-prismatic coordinated [Sm(en)4]3+ cation, a tetrahedral SbSe43, anion, and half a free en molecule in its asymmetric unit. The bandgaps of 2.22 eV for 1, 2.33 eV for 2, and 2.54 eV for 3 have been derived from optical absorption spectra. Compound 1 loses the en ligands in one step, whereas compound 2 loses them in two steps. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source]

    Reaction of Mercury(0) with the I2 Adduct of Tetraphenyldithioimidodiphosphinic Acid (SPPh2)2NH (HL) , Crystal Structures of [Hg(HL)I2] and HgL2

    M. Carla Aragoni
    Abstract The complex [Hg(HL)I2] (1) has been synthesised by reacting liquid Hg(0) in Et2O under mild reaction conditions with the I2 adduct of HL, HL·I2, while HgL2 (2) has been obtained from the reaction of compound 1 with HL in CH3CN. A single-crystal X-ray investigation of 1 shows four independent molecules in the asymmetric unit, each of which contains an HgII ion coordinated to two iodine atoms and two sulfur atoms of one bidentate neutral ligand in a distorted tetrahedral coordination geometry. Compound 2 consists of two anionic ligands coordinated to an HgII ion, which again displays a distorted tetrahedral coordination sphere. The reaction of 2 with HI (55 wt.-% in water) affords [Hg(HL)2](I)2 (3). Compounds 1, 2, and 3 have been characterised by FT-IR and 31P NMR spectroscopy. Density functional calculations suggest that compound 3 should feature a distorted tetrahedral coordination around the metal centre, with unequal Hg,S bond lengths. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source]

    Engineering of a monomeric and low-glycosylated form of human butyrylcholinesterase

    FEBS JOURNAL, Issue 2 2002
    Expression, characterization, crystallization, purification
    Human butyrylcholinesterase (BChE; EC is of particular interest because it hydrolyzes or scavenges a wide range of toxic compounds including cocaine, organophosphorus pesticides and nerve agents. The relative contribution of each N-linked glycan for the solubility, the stability and the secretion of the enzyme was investigated. A recombinant monomeric BChE lacking four out of nine N-glycosylation sites and the C-terminal oligomerization domain was stably expressed as a monomer in CHO cells. The purified recombinant BChE showed catalytic properties similar to those of the native enzyme. Tetragonal crystals suitable for X-ray crystallography studies were obtained; they were improved by recrystallization and found to diffract to 2.0 Å resolution using synchrotron radiation. The crystals belong to the tetragonal space group I422 with unit cell dimensions a = b = 154.7 Å, c = 124.9 Å, giving a Vm of 2.73 Å3 per Da (estimated 60% solvent) for a single molecule of recombinant BChE in the asymmetric unit. The crystal structure of butyrylcholinesterase will help elucidate unsolved issues concerning cholinesterase mechanisms in general. [source]

    Synthesis, Spectroscopic Studies, and Crystal Structures of Phenylorganotin Derivatives with [Bis(2,6-dimethylphenyl)amino]benzoic Acid: Novel Antituberculosis Agents

    Vaso Dokorou
    The novel triphenyl adduct of 2-[(2,6-dimethylphenyl)amino]benzoic acid (HDMPA; 1), i.e., [SnPh3(DMPA)] (2), the dimeric tetraorganostannoxane [Ph2(DMPA)SnOSn(DMPA)Ph2]2 (3), and the monomeric adduct [SnPh2(DMPA)2] (4), where DMPA is monodeprotonated HDMPA, have been prepared and structurally characterized by means of IR, 1H-NMR, and 13C-NMR spectroscopy. The structures of 1 and 2 have been determined by X-ray crystallography. Single-crystal X-ray-diffraction analysis of 1 revealed that there are two molecules in the asymmetric unit, HD1 and HD2, differing in conformation, both forming centrosymmetric dimers linked by H-bonds between the carboxylic O-atoms. X-Ray analysis of 2 revealed a pentacoordinate structure containing Ph3Sn coordinated to the carboxylato group. Significant CH/, interactions and intramolecular H-bonds stabilize the structures of 1 and 2, which self-assembled via CH/, and ,/, -stacking interactions. The Ph3Sn adduct 2 was found to be a promising antimycobacterial lead compound, displaying activity against Mycobacterium tuberculosis H37Rv. The cytotoxiciy in the Vero cell line is also reported. [source]

    Structures of Four Crystal Forms of Decaplanin

    Christopher Lehmann
    The glycopeptide antibiotic decaplanin (1; formerly known as MM 47761 and M86-1410) crystallizes in two P21 and two P6122 crystal forms, each with four monomers in the asymmetric unit, with solvent contents varying from 48 to 69%. Although with ca. 600 unique atoms, the structures are larger than typical small molecules, one was solved by direct methods. The other three were solved by typical macromolecular methods: single-wavelength anomalous diffraction (SAD) of the Cl-atoms present naturally in the structure, multiple-wavelength anomalous diffraction (MAD) at the Br absorption edge for a crystal soaked in NaBr solution, and molecular replacement. There is evidence of appreciable radiation damage with loss of 20,30% of the covalent and ionic halogens affecting the synchrotron datasets that may even have unintentionally facilitated the MAD structure solution. The structures contain the dimer units typical of antibiotics related to vancomycin, but, in addition, there are a variety of further intermolecular interactions responsible for the polymorphy leading to intertwined 61 -helices in two of the crystal forms. Except for the sugars and some sidechains, the conformations of the 16 independent monomers are very similar. [source]

    Crystal Structures and Magnetic Properties of Nitronyl Nitroxide Radicals

    Alexander Zakrassov
    The crystal structures and magnetic properties of the nitronyl nitroxide radicals 4,5-dihydro-4,4,5,5-tetramethyl-3-oxido(1H -imidazol-1-yloxyl) (1), 4,5-dihydro-2,4,4,5,5-pentamethyl-3-oxido(1H -imidazol-1-yloxyl) (2), 2-(4-chlorophenyl)-4,5-dihydro-4,4,5,5-tetramethyl-3-oxido(1H -imidazol-1-yloxyl) (3), and 4,5-dihydro-2-(2-hydroxy-5-nitrophenyl)-4,4,5,5-tetramethyl-3-oxido(1H -imidazol-1-yloxyl) (4) are reported. Compound 1 has two polymorphic forms: the , phase is monoclinic (P21/n space group), with a single molecule in the asymmetric unit, and the , phase is monoclinic (P21/c space group), with four molecules in the asymmetric unit. In the two polymorphs, the molecules are arranged in dimers formed by hydrogen bonds of the type CH,,,ON. The crystal structure of 3 contains layers of antiparallel ribbons of molecules. Compound 4 crystallizes with solvent molecules, and an intramolecular hydrogen bond is formed between the 2-OH group of the phenyl ring and the nitroxide O-atom. Compound 4 also loses the two O-atoms of the nitroxide moiety upon heating to 90°. Magnetic measurements showed that both , and , polymorphs of 1 exhibit antiferromagnetic coupling. The best fit to the experimental data was obtained using BleanyBower's singlet-triplet model (H=,2JSaSb): J=,11.2,K for the , phase and J=,15.0,K for the , phase. Compounds 3 and 4 show no evidence for spin coupling. [source]

    Parametric Rietveld refinement for the evaluation of powder diffraction patterns collected as a function of pressure

    Ivan Halasz
    Under the assumption that the structural parameters of a crystalline phase change `smoothly' with increasing pressure, the evolution of the parameters can be parameterized as a function of pressure using continuous monotonic functions. Four different approaches to determine the structural evolution of As2O5 with increasing pressure from a set of powder diffraction patterns collected over the pressure range from 2.5 to 19.5,GPa have been investigated. Approach (A) was the common sequential refinement of atomic coordinates with restraints on the geometry and was compared with three parameterization approaches. Approach (B) used direct parameterization by low-order polynomials of each crystallographically distinct atomic coordinate, (C) described the atoms of the asymmetric unit as a rigid body and allowed the internal degrees of freedom of the rigid body to vary with the change in pressure using rigid unit modes, and (D) described the crystal structure as a distortion of the higher-symmetry structure of As2O5 (which is here also a high-temperature phase) by using symmetry-adapted distortion modes. Approach (D) offers the possibility to directly introduce an order parameter into Rietveld refinement through an empirical power law derived from Landau theory and thus to obtain the value of the critical exponent. In contrast, the rigid-body approach did not fit the data as well. All parameterizations greatly reduce the number of required parameters. [source]

    ReX: a computer program for structural analysis using powder diffraction data

    Mauro Bortolotti
    Multi-platform software has been developed for the analysis of powder diffraction data, with particular focus on structure solution. The program provides a Rietveld optimization engine, with the possibility of refining parameters describing both the sample and the instrument model. Geometric constraints such as rigid fragments and torsion angles can be defined for the atomic structure, to reduce the number of degrees of freedom of the model. An innovative hierarchical description of the asymmetric unit has been adopted, which allows, in principle, the definition of arbitrarily complex geometric relationships. Additionally, global optimization algorithms may be used in place of the standard nonlinear least squares, when particularly challenging problems are being faced. [source]

    Crystal-state 3D-structural characterization of novel 310 -helical peptides

    Dr Marco Crisma
    Abstract The crystal-state conformations of two octapeptides, pBrBz-(D -Iva)8 -OtBu (8I) and Ac-[L -(,Me)Val]8 -OH (8II), the heptapeptide Z-[L -(,Me)Val]7 -OH (7), the hexapeptide Z-[L -(,Me)Leu]6 -OtBu (6) and the tetrapeptide alkylamide Z-(Aib)2 - L -Glu(OMe)- L -Ala- L -Lol (5) were assessed by x-ray diffraction analyses. Two independent molecules are observed in the asymmetric unit of each L -(,Me)Val homo-peptide. All four homo-peptides are folded in a regular 310 -helical structure (only the C -terminal H-bonded conformation of the D -Iva octapeptide is distorted to a type-I ,-turn). The hydroxyl groups of the C -terminal carboxyl moieties of the two L -(,Me)Val homo-peptides participate in an oxy-analogue of the type-III ,-turn conformation. While the two L -(,Me)Val 310 -helices are right-handed, the D -Iva and L -(,Me)Leu helices are left-handed. The tetrapeptide alkylamide is 310 -helical at the N -terminus, but it is mixed 310/,-helical at the C -terminus. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd. [source]

    Novel dimer structure of a membrane-bound protease with a catalytic Ser,Lys dyad and its linkage to stomatin

    Hideshi Yokoyama
    Membrane-bound proteases are involved in various regulatory functions. A previous report indicates that the N-terminal region of PH1510 (1510-N) from the hyperthermophilic archaeon Pyrococcus horikoshii is a serine protease with a catalytic Ser,Lys dyad (Ser97 and Lys138), and specifically cleaves the C-terminal hydrophobic region of the p-stomatin PH1511. According to the crystal structure of the wild-type 1510-N in dimeric form, the active site around Ser97 is in a hydrophobic environment suitable for the hydrophobic substrates. This article reports the crystal structure of the K138A mutant of 1510-N at 2.3,Å resolution. The determined structure contains one molecule per asymmetric unit, but 1510-N is active in dimeric form. Two possible sets of dimer were found from the symmetry-related molecules. One dimer is almost the same as the wild-type 1510-N. Another dimer is probably in an inactive form. The L2 loop, which is disordered in the wild-type structure, is significantly kinked at around A-138 in the K138A mutant. Thus Lys138 probably has an important role on the conformation of L2. [source]

    Diffusion-equation method for crystallographic figure of merits

    Anders J. Markvardsen
    Global optimization methods play a significant role in crystallography, particularly in structure solution from powder diffraction data. This paper presents the mathematical foundations for a diffusion-equation-based optimization method. The diffusion equation is best known for describing how heat propagates in matter. However, it has also attracted considerable attention as the basis for global optimization of a multimodal function [Piela et al. (1989). J. Phys. Chem.93, 3339,3346]. The method relies heavily on available analytical solutions for the diffusion equation. Here it is shown that such solutions can be obtained for two important crystallographic figure-of-merit (FOM) functions that fully account for space-group symmetry and allow the diffusion-equation solution to vary depending on whether atomic coordinates are fixed or not. The resulting expression is computationally efficient, taking the same order of floating-point operations to evaluate as the starting FOM function measured in terms of the number of atoms in the asymmetric unit. This opens the possibility of implementing diffusion-equation methods for crystallographic global optimization algorithms such as structure determination from powder diffraction data. [source]

    Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms

    PROTEIN SCIENCE, Issue 4 2010
    Jonathan M. Elkins
    Abstract PDZ domains most commonly bind the C-terminus of their protein targets. Typically the C-terminal four residues of the protein target are considered as the binding motif, particularly the C-terminal residue (P0) and third-last residue (P-2) that form the major contacts with the PDZ domain's "binding groove". We solved crystal structures of seven human PDZ domains, including five of the seven PDLIM family members. The structures of GRASP, PDLIM2, PDLIM5, and PDLIM7 show a binding mode with only the C-terminal P0 residue bound in the binding groove. Importantly, in some cases, the P-2 residue formed interactions outside of the binding groove, providing insight into the influence of residues remote from the binding groove on selectivity. In the GRASP structure, we observed both canonical and noncanonical binding in the two molecules present in the asymmetric unit making a direct comparison of these binding modes possible. In addition, structures of the PDZ domains from PDLIM1 and PDLIM4 also presented here allow comparison with canonical binding for the PDLIM PDZ domain family. Although influenced by crystal packing arrangements, the structures nevertheless show that changes in the positions of PDZ domain side-chains and the ,B helix allow noncanonical binding interactions. These interactions may be indicative of intermediate states between unbound and fully bound PDZ domain and target protein. The noncanonical "perpendicular" binding observed potentially represents the general form of a kinetic intermediate. Comparison with canonical binding suggests that the rearrangement during binding involves both the PDZ domain and its ligand. [source]

    Crystal packing of a bacteriophage MS2 coat protein mutant corresponds to octahedral particles

    PROTEIN SCIENCE, Issue 10 2008
    Pavel Plevka
    Abstract A covalent dimer of the bacteriophage MS2 coat protein was created by performing genetic fusion of two copies of the gene while removing the stop codon of the first gene. The dimer was crystallized in the cubic F432 space group. The organization of the asymmetric unit together with the F432 symmetry results in an arrangement of subunits that corresponds to T = 3 octahedral particles. The octahedral particles are probably artifacts created by the particular crystal packing. When it is not crystallized in the F cubic crystal form, the coat protein dimer appears to assemble into T = 3 icosahedral particles indistinguishable from the wild-type particles. To form an octahedral particle with closed surface, the dimer subunits interact at sharper angles than in the icosahedral arrangement. The fold of the covalent dimer is almost identical to the wild-type dimer with differences located in loops and in the covalent linker region. The main differences in the subunit packing between the octahedral and icosahedral arrangements are located close to the fourfold and fivefold symmetry axes where different sets of loops mediate the contacts. The volume of the wild-type virions is 7 times bigger than that of the octahedral particles. [source]

    Crystal structure of enoyl,acyl carrier protein reductase (FabK) from Streptococcus pneumoniae reveals the binding mode of an inhibitor

    PROTEIN SCIENCE, Issue 4 2008
    Jun Saito
    Abstract Enoyl,acyl carrier protein (ACP) reductases are critical for bacterial type II fatty acid biosynthesis and thus are attractive targets for developing novel antibiotics. We determined the crystal structure of enoyl,ACP reductase (FabK) from Streptococcus pneumoniae at 1.7 Å resolution. There was one dimer per asymmetric unit. Each subunit formed a triose phosphate isomerase (TIM) barrel structure, and flavin mononucleotide (FMN) was bound as a cofactor in the active site. The overall structure was similar to the enoyl,ACP reductase (ER) of fungal fatty acid synthase and to 2-nitropropane dioxygenase (2-ND) from Pseudomonas aeruginosa, although there were some differences among these structures. We determined the crystal structure of FabK in complex with a phenylimidazole derivative inhibitor to envision the binding site interactions. The crystal structure reveals that the inhibitor binds to a hydrophobic pocket in the active site of FabK, and this is accompanied by induced-fit movements of two loop regions. The thiazole ring and part of the ureido moiety of the inhibitor are involved in a face-to-face ,,, stacking interaction with the isoalloxazine ring of FMN. The side-chain conformation of the proposed catalytic residue, His144, changes upon complex formation. Lineweaver,Burk plots indicate that the inhibitor binds competitively with respect to NADH, and uncompetitively with respect to crotonoyl coenzyme A. We propose that the primary basis of the inhibitory activity is competition with NADH for binding to FabK, which is the first step of the two-step ping-pong catalytic mechanism. [source]

    Crystal structure of a dimeric form of streptococcal pyrogenic exotoxin A (SpeA1)

    PROTEIN SCIENCE, Issue 9 2004
    Matthew D. Baker
    Abstract Streptococcal pyrogenic exotoxin A (SpeA1) is a bacterial superantigen associated with scarlet fever and streptococcal toxic shock syndrome (STSS). SpeA1 is found in both monomeric and dimeric forms, and previous work suggested that the dimer results from an intermolecular disulfide bond between the cysteines at positions 90 of each monomer. Here, we present the crystal structure of the dimeric form of SpeA1. The toxin crystallizes in the orthorhombic space group P212121, with two dimers in the crystallographic asymmetric unit. The final structure has a crystallographic R-factor of 21.52% for 7248 protein atoms, 136 water molecules, and 4 zinc atoms (one zinc atom per molecule). The implications of SpeA1 dimer on MHC class II and T-cell receptor recognition are discussed. [source]

    Structural features of a zinc binding site in the superantigen strepococcal pyrogenic exotoxin A (SpeA1): Implications for MHC class II recognition

    PROTEIN SCIENCE, Issue 6 2001
    Matthew Baker
    Abstract Streptococcal pyrogenic exotoxin A (SpeA) is produced by Streptococcus pyogenes, and has been associated with severe infections such as scarlet fever and Streptococcal Toxic Shock Syndrome (STSS). In this study, the crystal structure of SpeA1 (the product of speA allele 1) in the presence of 2.5 mM zinc was determined at 2.8 Å resolution. The protein crystallizes in the orthorhombic space group P21212, with four molecules in the crystallographic asymmetric unit. The final structure has a crystallographic R -factor of 21.4% for 7,031 protein atoms, 143 water molecules, and 4 zinc atoms (one zinc atom per molecule). Four protein ligands,Glu 33, Asp 77, His 106, and His 110,form a zinc binding site that is similar to the one observed in a related superantigen, staphylococcoal enterotoxin C2. Mutant toxin forms substituting Ala for each of the zinc binding residues were generated. The affinity of these mutants for zinc ion confirms the composition of this metal binding site. The implications of zinc binding to SpeA1 for MHC class II recognition are explored using a molecular modeling approach. The results indicate that, despite their common overall architecture, superantigens appear to have multiple ways of complex formation with MHC class II molecules. [source]

    Convergence study of a Schrödinger-equation algorithm and structure-factor determination from the wavefunction

    Kostas Bethanis
    The algorithm [Bethanis, Tzamalis, Hountas & Tsoucaris (2002). Acta Cryst. A58, 265,269] which reformulates the quantum-mechanical problem of solving a Schrödinger (S) equation in a crystallographic context has been upgraded and tested for many aspects of convergence. The upgraded algorithm in reciprocal space aims at determining a wavefunction ,H such that (a) ,H fulfils the S equation within certain precision and (b) ,H minimizes by least squares the differences between the calculated structure factors from the wavefunction and the observed ones. Calculations have been made with three molecules (11, 41 and 110 non-H atoms in the asymmetric unit) for different numbers of initially given phases. Three main questions have been addressed: (I) Does the iterative calculation of the wavefunction converge? (II) Do the calculated wavefunctions converge to a unique set of ,H values independent of the initial random set of ,H? (III) Is the calculated ,H set a good approximation of a wavefunction able to produce within certain errors the correct values of the phases of the structure factors? Concerning questions (I) and (II), our results give a strong hint about fast convergence to a unique wavefunction independent of the arbitrary starting wavefunction. This is an essential prerequisite for practical applications. For question (III) in the case closer to the ab initio situation, the final mean phase error, respectively, for the three structures is 3, 26 and 28°. The combination of (a) and (b) in the upgraded algorithm has been proved crucial especially for the results concerning the larger structures. [source]

    Introduction to a general crystallography

    A. Janner
    The definition of an extended crystallographic group is given, based on an -dimensional Euclidean space, carrier of a faithful integral representation of a permutation group of atomic positions. The Euclidean crystallography of normal crystals and the higher-dimensional one applied to incommensurately modulated crystals, intergrowth crystals and quasicrystals are special cases of a general crystallography. The same is true for the multimetrical crystallographic characterization of ice and of snow crystals. This approach can also be applied to single molecules, leading to what may be denoted as molecular crystallography. It possibly allows non-trivial structural relations between atomic positions belonging to the asymmetric unit of the molecular point group to be obtained. Two simple molecules, polycyclic aromatic hydrocarbons, are treated as illustrative examples. [source]

    Structures of alkyl-substituted Tröger's base derivatives illustrate the importance of Z, for packing in the absence of strong crystal synthons

    Christophe M. L. Vande Velde
    Crystal structures of Tröger's base (5,11-methano-2,8-dimethyl-5,6,11,12-tetrahydrodibenzo[b,f][1,5]diazocine) analogues with the methyl groups replaced by ethyl, iso -propyl and tert -butyl groups were studied. The incidence of Z, > 1 structures increases to rather conspicuous levels. The reasons behind this trend are expanded upon, and a possible explanation is given in the flexibility of the alkyl substituents and van der Waals stabilization. In combination these effects allow for an additional stabilization of the packing by small changes in the molecular conformations, thus expanding the size of the asymmetric unit. [source]

    1,1,-Fc(4-C6H4CO2Et)2 and its unusual salt derivative with Z, = 5, catena -[Na+]2[1,1,-Fc(4-C6H4CO2,)2]·0.6H2O [1,1,-Fc = (,5 -(C5H4)2Fe]

    John F. Gallagher
    The neutral diethyl 4,4,-(ferrocene-1,1,-diyl)dibenzoate, Fe[,5 -(C5H4)(4-C6H4CO2Et)]2 (I), yields (II) (following base hydrolysis) as the unusual complex salt poly[disodium bis[diethyl 4,4,-(ferrocene-1,1,-diyl)dibenzoate] 0.6-hydrate] or [Na+]2[Fe{,5 -(C5H4)-4-C6H4CO}2]·0.6H2O with Z, = 5. Compound (I) crystallizes in the triclinic system, space group , with two molecules having similar geometry in the asymmetric unit (Z, = 2). The salt complex (II) crystallizes in the orthorhombic system, space group Pbca, with the asymmetric unit comprising poly[decasodium pentakis[diethyl 4,4,-(ferrocene-1,1,-diyl)dibenzoate] trihydrate] or [Na+]10[Fe{,5 -(C5H4)-4-C6H4CO}2]5·3H2O. The five independent 1,1,-Fc[(4-C6H4CO2),]2 dianions stack in an offset ladder (stepped) arrangement with the ten benzoates mutually oriented cisoid towards and bonded to a central layer comprising the ten Na+ ions and three water molecules [1,1,-Fc = ,5 -(C5H4)2Fe]. The five dianions differ in the cisoid orientations of their pendant benzoate groups, with four having their ,C6H4, groups mutually oriented at interplanar angles from 0.6,(3) to 3.2,(3)° (as ,..., stacked C6 rings) and interacting principally with Na+ ions. The fifth dianion is distorted and opens up to an unprecedented ,C6H4, interplanar angle of 18.6,(3)° through bending of the two 4-C6H4CO2 groups and with several ionic interactions involving the three water molecules (arranged as one-dimensional zigzag chains in the lattice). Overall packing comprises two-dimensional layers of Na+ cations coordinated mainly by the carboxylate O atoms, and one-dimensional water chains. The non-polar Fc(C6H4)2 groups are arranged perpendicular to the layers and mutually interlock through a series of efficient C,H..., stacking contacts in a herringbone fashion to produce an overall segregation of polar and non-polar entities. [source]

    l -2-Aminobutyric acid: two fully ordered polymorphs with Z, = 4

    Carl Henrik Görbitz
    The crystal structure of l -2-aminobutyric acid, an l -alanine analogue with an ethyl rather than a methyl side chain, has proved elusive owing to problems growing diffraction quality crystals. Good diffraction data have now been obtained for two polymorphs, in space groups P21 and I2, revealing surprisingly complex, yet fully ordered crystalline arrangements with Z, = 4. The closely related structures are divided into hydrophilic and hydrophobic layers, the latter being the thinnest ever found for an amino acid (other than ,-glycine). The hydrophobic layers furthermore contain conspicuous pseudo-centers-of-symmetry, leading to overall centrosymmetric intensity statistics. Uniquely, the four molecules in the asymmetric unit can be divided into two pairs that each forms an independent hydrogen-bond network. [source]

    Concomitant polymorphic behavior of di-,-thiocyanato-,2N:S;,2S:N -bis[bis(tri- p -fluorophenylphosphine-,P)silver(I)]

    Bernard Omondi
    The structures of two polymorphs, both monoclinic P21/n [polymorph (I)] and P21/c [polymorph (II)], of di-,-thiocyanato-,2N:S;,2S:N -bis[bis(tri- p -fluorophenylphosphine-,P)silver(I)] complexes have been determined at 100,K. In both polymorphs the complex has a dinuclear structure where the silver(I) coordinates to two phosphine ligands and two bridging thiocyanate anions to form complexes with distorted tetrahedral geometry. Polymorph (I) has just one half of the [Ag2(SCN)2{P(4-FC6H4)3}4] molecule at (0, ½, 0) from the origin in the asymmetric unit. Polymorph (II) has one and a half molecules of [Ag2(SCN)2{P(4-FC6H4)3}4] in the asymmetric unit; the half molecule is situated at (0, 1, ½), while the full molecule is located at (1/3, ½, 1/3) from the origin. The Ag,P bond distances range from 2.4437,(4) to 2.4956,(7),Å in both polymorphs. The Ag,S distances are 2.5773,(7),Å in (I) and 2.5457,(5), 2.5576,(5) and 2.5576,(5),Å in (II). The full molecule in polymorph (II) has slightly shorter Ag,N bond distances [2.375,(1) and 2.367,(2),Å] compared with the half molecules in both polymorphs [2.409,(2),Å in (II) and 2.395,(2),Å in (I)]. The two polymorphs are compared using r.m.s. overlay calculations as well as half-normal probability plot analysis. [source]

    A solution to the observed Z, = 2 preference in the crystal structures of hydrophobic amino acids

    Carl Henrik Görbitz
    Chiral amino acids without functional groups in their side chains (hydrophobic amino acids) systematically form crystals with two molecules in the asymmetric unit. In contrast, racemates of the same compounds form crystals with Z, = 1. The present investigation addresses the origin of this important difference between enantiomeric and racemic crystals. Through a series of ab initio calculations on infinite two-dimensional slabs, derived from crystal structures, as well as calculations on full crystal structures it is shown that it is indeed possible to explain the observed behaviour. Additionally, the (not unexpected) observation that amino acids usually form racemates in the solid phase rather than undergoing racemic separation upon crystallization is rationalized on the basis of energy calculations. [source]

    Structures of mono-unsaturated triacylglycerols.


    The , -2 crystal structures of a series of mixed-chain saturated and trans -mono-unsaturated triacylglycerols containing palmitoyl, stearoyl and elaidoyl acyl chains have been solved from high-resolution powder diffraction data, from synchrotron as well as laboratory X-ray sources. The structures crystallized in the space group I2 with two independent molecules forming a dimer in the asymmetric unit, and packed in double-chain length layers. Unlike the corresponding ,-2 structures the solved , -2 structures have different molecular conformations for the symmetric and the asymmetric mixed triacylglycerols, both with the sn -2 chain in a leg position of the chair-shaped conformation. A transformation to the ,-2 structure with the sn -2 chain in the back position is complicated and unlikely to take place in the solid state. A novel ,,-2 polymorph of PSS has been crystallized and its structure has been solved. The melting point (239,K) of this so-called , -2 polymorph is 2,K above that of the , -2 polymorph and almost equal to that of the ,-2 polymorph of PSS. The difference in packing of the , -2 versus, -2 structure explains the slow , -2 to , -2 phase transition. The transition is strikingly similar to the ,2 -3 to ,1 -3 transition in cis -mono-unsaturated triacylglycerols. [source]

    Order,disorder twinning model and stacking faults in ,-NTO

    Dieter Schwarzenbach
    Crystals of the recently published [Bolotina, Kirschbaum & Pinkerton (2005). Acta Cryst. B61, 577,584] triclinic (P) structure of 5-nitro-2,4-dihydro-1,2,4-triazol-3-one (,-NTO) occur as fourfold twins. There are Z, = 4 independent molecules per asymmetric unit. We show that the structure contains layers with 2-periodic layer-group symmetry p21/b 1 (1). This symmetry is lost through the stacking of the layers, which is a possible explanation for Z, = 4. A layer can assume four different but equivalent positions with respect to its nearest neighbor. Twinning arises through stacking faults and is an instructive example of the application of order,disorder theory using local symmetry operations. The near-neighbor relations between molecules remain unchanged through all twin boundaries. The four structures with maximum degree of order, one of which is the observed one, and the family reflections common to all domains are identified. Rods of weak diffuse scattering confirm the stacking model. [source]

    S,S -1,2-Dicyclohexylethane-1,2-diol and its racemic compound: a striking exception to Wallach's rule

    Brian O. Patrick
    The structures of enantiopure S,S -1,2-dicyclohexylethane-1,2-diol and its racemic compound (rac - S,S -1,2-dicyclohexyl­ethane-1,2-diol) have been determined at 295 and 173,K. The crystals of the enantiopure material are more than 4% denser than the crystals of the racemic compound, but the melting points indicate that the crystals of the less dense racemic compound are considerably more stable than those of the racemic conglomerate. This apparent exception to the correlation of crystal density and melting point is explained. The enantiopure crystals have four molecules in the asymmetric unit (Z, = 4). Two of the molecules have the conformation observed for the one independent molecule of the racemic compound and two have a higher energy conformation; the overall P21 structure is a perturbed version of a P212121 structure with Z, = 2. The enantiopure and racemic crystals have the same hydrogen-bonding motif, but the motif in the former appears to be significantly strained. A reason why crystals of enantiopure material might be systematically less dense than crystals of its racemic compound and to be more likely to have Z, > 1 is suggested. [source]