Group P21 (group + p21)

Distribution by Scientific Domains

Kinds of Group P21

  • monoclinic space group p21
  • primitive monoclinic space group p21
  • space group p21

  • Selected Abstracts

    Synthesis and crystal structure investigation of pyridine-2-(3,-mercaptopropanoic acid)- N -oxide

    R. Ramasubramanian
    Abstract Pyridine-2-(3,-mercaptopropanoic acid)- N -oxide (I), is a higher homologue of 1-oxopyridinium-2-thioacetic acid (II) [1]. It crystallizes in monoclinic space group P21 with a = 9.2168(2) Å, b = 4.1423(2) Å, c = 11.3904(4) Å, , = 98.65(2)°, V = 429.93(3) Å3 and Z = 2. The least-squares refinement gave residual index R = 0.024 for 1070 observed reflections. The introduction of an additional methylene group in (II) causes a flip in the carboxylic acid group of (I) that facilitates the molecules to align infinite antiparallel chains through strong C,H···O interactions. The molecules are interlinked by O,H···O hydrogen bonding across the chains and forming an infinite screw chain along y-direction. The molecular packing is stabilized by O,H···O and C,H···O hydrogen bonding and ,-, electron interactions. This is an important facet of the crystal packing. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

    New Organic Nonlinear Optical Polyene Crystals and Their Unusual Phase Transitions,

    O-P. Kwon
    Abstract A series of new nonlinear optical chromophores based on configurationally locked polyenes (CLPs) with chiral pyrrolidine donors are synthesized. All CLP derivatives exhibit high thermal stability with decomposition temperatures Td at least > ,270,°C. Acentric single crystals of enantiopure D - and L -prolinol-based chromophores with a monoclinic space group P21 exhibit a macroscopic second-order nonlinearity that is twice as large than that of analogous dimethylamino-based crystal. This is attributed to a strong hydrogen-bonded polar polymer-like chain built by these molecules, which is aligned along the polar crystallographic b -axis. Five ,-phase CLP crystals with different donors grown from solution exhibit a reversible or irreversible thermally induced structural phase transition to a ,-phase. These phase transitions are unusual, changing the crystal symmetry from higher to lower at increasing temperatures, for example, from centrosymmetric to non-centrosymmetric, enhancing their macroscopic second-order nonlinear optical properties. [source]

    Guest-Induced Chirality in the Ferrimagnetic Nanoporous Diamond Framework Mn3(HCOO)6,

    B. Zhang
    Abstract Chiral magnets are obtained by inclusion of chiral guest molecules into the channels of an achiral nanoporous ferrimagnet consisting of the Mn3(HCOO)6 (1) framework. Insertion of the R or the S enantiomer of 2-chloropropan-1-ol (CH3C*HClCH2OH) in the chiral pores of the previously emptied framework (space group P21/c) results in the two corresponding chiral solids (1R and 1S, space group P21), while insertion of a racemic mixture of the two enantiomers retains the achirality of the host for the meso solid (1RS, space group P21/c). The R guest is ordered in the M channels while the S guest is ordered in the P channels. In contrast, the R guests in the P channels and the S guests in the M channels are disordered on two crystallographic orientations. For the racemic mixture of the two enantiomers in 1RS, random disorder of guests in both channels is observed. Thus, the localization of the guest molecule depends on the nature of the surface to recognize the guest of a particular chirality. The guest inclusion compounds are thermally stable. The 1R and 1S compounds are optically active. All the compounds adopt a ferrimagnetic ground state. Compared to the host framework of 1 without guest, the Curie temperature decreases for both 1R and 1S but increases for 1RS. The additional interactions between the framework and the inserted guest alcohols strengthen the lattice via hydrogen bonds and other electrostatic forces, and it might account for the significant lowering of the lattice contribution as well as the magnetic component to the specific heat capacity upon guest loading. [source]

    Zinc Vanadates in Vanadium Oxide-Doped Zinc Oxide Varistors

    Huey-Hoon Hng
    Convergent-beam electron diffraction has been used to determine the space groups of ,- and ,-Zn3(VO4)2 particles in vanadium oxide-doped zinc oxide varistors. The crystal structure of ,-Zn3(VO4)2 has been determined to be monoclinic with space group P21 and lattice parameters of a= 9.80 Å, b= 8.34 Å, c= 10.27 Å, and ,= 115.8°, whereas that of ,-Zn3(VO4)2 is monoclinic with space group Cm and a= 10.40 Å, b= 8.59 Å, c= 9.44 Å, and ,= 98.8°. Energy-dispersive X-ray microanalysis of these two phases shows significant deviations from their expected stoichiometry. It is apparent that the ,-phase is, in fact, the metastable Zn4V2O9 phase, whereas the ,-phase either is a new oxide that consists of zinc, vanadium, and manganese or, more likely, is a zinc vanadate phase with a Zn:V atomic ratio of 1:1 that has the ability to go into solid solution with manganese. [source]

    Structures of the OmpF porin crystallized in the presence of foscholine-12

    PROTEIN SCIENCE, Issue 5 2010
    Georgia Kefala
    Abstract The endogenous Escherichia coli porin OmpF was crystallized as an accidental by-product of our efforts to express, purify, and crystallize the E. coli integral membrane protein KdpD in the presence of foscholine-12 (FC12). FC12 is widely used in membrane protein studies, but no crystal structure of a protein that was both purified and crystallized with this detergent has been reported in the Protein Data Bank. Crystallization screening for KdpD yielded two different crystals of contaminating protein OmpF. Here, we report two OmpF structures, the first membrane protein crystal structures for which extraction, purification, and crystallization were done exclusively with FC12. The first structure was refined in space group P21 with cell parameters a = 136.7 Å, b = 210.5 Å, c = 137 Å, and , = 100.5°, and the resolution of 3.8 Å. The second structure was solved at the resolution of 4.4 Å and was refined in the P321 space group, with unit cell parameters a = 215.5 Å, b = 215.5 Å, c = 137.5 Å, and , = 120°. Both crystal forms show novel crystal packing, in which the building block is a tetrahedral arrangement of four trimers. Additionally, we discuss the use of FC12 for membrane protein crystallization and structure determination, as well as the problem of the OmpF contamination for membrane proteins overexpressed in E. coli. [source]

    Isomeric N -(iodophenyl)nitrobenzamides form different three-dimensional framework structures

    James L. Wardell
    The isomeric N -(iodophenyl)nitrobenzamides, C13H9IN2O3, all form different three-dimensional framework structures. Molecules of N -(2-iodophenyl)-3-nitrobenzamide (II) are linked by a combination of N,H,O and C,H,O hydrogen bonds and a two-centre iodo,carbonyl interaction. The supramolecular structure of N -(2-iodophenyl)-4-nitrobenzamide (III) is built from one N,H,O and two C,H,O hydrogen bonds, but short I,O contacts are absent from the structure. In N -(3-iodophenyl)-2-nitrobenzamide (IV), which crystallizes with Z, = 2 in space group P21, the structure contains two N,H,O hydrogen bonds, four C,H,O hydrogen bonds, two two-centre iodo,nitro interactions and an aromatic ,,, stacking interaction. The structure of N -(3-iodophenyl)-3-nitrobenzamide (V) contains one N,H,O hydrogen bond and three C,H,O hydrogen bonds, together with a two-centre iodo,nitro interaction and an aromatic ,,, stacking interaction, while in N -(3-iodophenyl)-4-nitrobenzamide (VI), the combination of one N,H,O hydrogen bond and two C,H,O hydrogen bonds is augmented not only by a two-centre iodo,nitro interaction and an aromatic ,,, stacking interaction, but also by a dipolar carbonyl,carbonyl interaction. In the supramolecular structure of N -(4-iodophenyl)-4-nitrobenzamide (IX), which crystallizes with Z, = 2 in space group , there are two N,H,O hydrogen bonds, four C,H,O hydrogen bonds and two three-centre iodo,nitro interactions. [source]

    Topochemically controlled solid-state methyl ­rearrangement in thiocyanurates

    Mark Greenberg
    4,6-Dimethoxy-3-methyl-1,3,5-triazine-2(3H)-thione crystallizes in two polymorphic forms, needles and plates. In the needle-shaped crystals (9a) the molecules occupy the crystallographic mirror plane, thus the layers are stacked along the b axis. The molecules of the other polymorph [plate-shape crystals, (9b)] are packed in a herringbone packing mode. Upon heating, (9b) undergoes a phase transition to form (9a). At 378,K the needles undergo O , S topochemically controlled methyl transfer in the solid state to produce 1-methyl-4-methoxy-6-methylthio-1,3,5-triazine-2(1H)-one in 75% yield. The enthalpy of the rearrangement is estimated to be ,39.1,kJ,mol,1. 1-Methyl-6-methoxy-4-methylthio-1,3,5-triazine-2(1H)-thione crystallizes in space group P21 with two crystallographically independent molecules in the asymmetric unit. Compound (9b) undergoes O , S methyl transfer in the solid state at 373,K. The rearrangement is topochemically assisted and the product, 1-methyl-2,4-bismethylthio-1,3,5-triazine-6(1H)-one, is obtained in quantitative yield. The enthalpy of the rearrangement is estimated to be ,58.8,kJ,mol,1. The crystal structures of the compounds as well as their DSC thermographs are described and discussed. Energy calculation by ab initio methods shows that the driving force for the reactions is the difference between the molecular energies of the pre-rearranged compounds and their products, 54.2 and 59.3,kJ,mol,1 in the two cases, respectively. [source]

    Hydrogen-bonded dimers, chains and rings in six differently substituted 2-vinyltetrahydro-1,4-epoxy-1-benzazepines

    Lina M. Acosta
    In (2SR,4RS)-2- exo -vinyl-2,3,4,5-tetrahydro-1H -1,4-epoxy-1-benzazepine, C12H13NO, (I), the molecules are linked by two independent C,H...,(arene) hydrogen bonds to form sheets, such that all of the molecules in a given sheet are of the same configuration. The molecules of (2SR,4RS)-7-chloro-2- exo -(2-methylprop-1-enyl)-2,3,4,5-tetrahydro-1H -1,4-epoxy-1-benzazepine, C14H16ClNO, (II), are linked by a C,H...O hydrogen bond into C(4) chains, where all the molecules in a given chain are of the same configuration, whereas the molecules of (2SR,4RS)-8-chloro-9-methyl-2- exo -(2-methylprop-1-enyl)-2,3,4,5-tetrahydro-1H -1,4-epoxy-1-benzazepine, C15H18ClNO, (III), are linked into centrosymmetric dimers by pairs of symmetry-related C,H...,(arene) hydrogen bonds. (2RS,4RS)-8-Chloro-9-methyl-2- endo -(2-methylprop-1-enyl)-2,3,4,5-tetrahydro-1H -1,4-epoxy-1-benzazepine, C15H18ClNO, (IV), is a diastereoisomer of (III) and, as for (II), a single C,H...O hydrogen bond links the molecules into C(4) chains, each containing molecules of a single configuration. The structure of (2SR,4RS)-8-chloro-9-methyl-2- exo -(prop-1-en-2-yl)-2,3,4,5-tetrahydro-1H -1,4-epoxy-1-benzazepine, C14H16ClNO, (V), contains a C,H...O hydrogen bond which links pairs of molecules into centrosymmetric R22(6) dimers. (2SR,4RS)-7,9-Dichloro-2- exo -(prop-1-en-2-yl)-2,3,4,5-tetrahydro-1H -1,4-epoxy-1-benzazepine, C13H13Cl2NO, (VI), is an inversion twin containing both the (2S,4R) and (2R,4S) enantiomers in the space group P21, and a C,H...O hydrogen bond links molecules of a given configuration into simple C(3) chains. [source]

    Eight 7-benzyl-3- tert -butyl-1-phenylpyrazolo[3,4- d]oxazines, encompassing structures containing no intermolecular hydrogen bonds, and hydrogen-bonded structures in one, two or three dimensions

    Juan C. Castillo
    7-Benzyl-3- tert -butyl-1-phenyl-6,7-dihydro-1H,4H -pyrazolo[3,4- d][1,3]oxazine, C22H25N3O, (I), and 3- tert -butyl-7-(4-methylbenzyl)-1-phenyl-6,7-dihydro-1H,4H -pyrazolo[3,4- d][1,3]oxazine, C23H27N3O, (II), are isomorphous in the space group P21, and molecules are linked into chains by C,H...O hydrogen bonds. In each of 3- tert -butyl-7-(4-methoxybenzyl)-1-phenyl-6,7-dihydro-1H,4H -pyrazolo[3,4- d][1,3]oxazine, C23H27N3O2, (III), which has cell dimensions rather similar to those of (I) and (II), also in P21, and 3- tert -butyl-1-phenyl-7-[4-(trifluoromethyl)benzyl]-6,7-dihydro-1H,4H -pyrazolo[3,4- d][1,3]oxazine, C23H24F3N3O, (IV), there are no direction-specific interactions between the molecules. In 3- tert -butyl-7-(4-nitrobenzyl)-1-phenyl-6,7-dihydro-1H,4H -pyrazolo[3,4- d][1,3]oxazine, C22H24N4O3, (V), a combination of C,H...O and C,H...N hydrogen bonds links the molecules into complex sheets. There are no direction-specific interactions between the molecules of 3- tert -butyl-7-(2,3-dimethoxybenzyl)-1-phenyl-6,7-dihydro-1H,4H -pyrazolo[3,4- d][1,3]oxazine, C24H29N3O3, (VI), but a three-dimensional framework is formed in 3- tert -butyl-7-(3,4-methylenedioxybenzyl)-1-phenyl-6,7-dihydro-1H,4H -pyrazolo[3,4- d][1,3]oxazine, C23H25N3O3, (VII), by a combination of C,H...O, C,H...N and C,H...,(arene) hydrogen bonds, while a combination of C,H...O and C,H...,(arene) hydrogen bonds links the molecules of 3- tert -butyl-1-phenyl-7-(3,4,5-trimethoxybenzyl)-6,7-dihydro-1H,4H -pyrazolo[3,4- d][1,3]oxazine, C25H31N3O4, (VIII), into complex sheets. In each compound, the oxazine ring adopts a half-chair conformation, while the orientations of the pendent phenyl and tert -butyl substituents relative to the pyrazolo[3,4- d]oxazine unit are all very similar. [source]

    Coordination behaviour and two-dimensional-network formation in poly[[,-aqua-diaqua(,5 -propane-1,3-diyldinitrilotetraacetato)dilithium(I)cobalt(II)] dihydrate]: the first example of an MII,1,3-pdta complex with a monovalent metal counter-ion

    Urszula Rychlewska
    The title compound, {[CoLi2(C11H14N2O8)(H2O)3]·2H2O}n, constitutes the first example of a salt of the [MII(1,3-pdta)]2, complex (1,3-pdta is propane-1,3-diyldinitrilotetraacetate) with a monopositive cation as counter-ion. Insertion of the Li+ cation could only be achieved through application of the ion-exchange column technique which, however, appeared unsuccessful with other alkali metals and the ammonium cation. The structure contains two tetrahedrally coordinated Li+ cations, an octahedral [Co(1,3-pdta)]2, anion and five water molecules, two of which are uncoordinated, and is built of two-dimensional layers extending parallel to the (010) lattice plane, the constituents of which are connected by the coordinate bonds. O,Hwater...O hydrogen bonds operate both within and between these layers. The crystal investigated belongs to the enantiomeric space group P21 with only one (,) of two possible optical isomers of the [Co(1,3-pdta)]2, complex. A possible cause of enantiomer separation during crystallization might be the rigidification and polarization of the [M(1,3-pdta)]2, core, resulting from direct coordination of Li+ cations to three out of four carboxylate groups constituting the 1,3-pdta ligand. The structure of (I) differs considerably from those of the other [MII(1,3-pdta)]2, complexes, in which the charge compensation is realized by means of divalent hexaaqua complex cations. This finding demonstrates a significant structure-determining role of the counter-ions. [source]

    N -(2-Carboxy­benzoyl)- l -leucine methyl ester

    Alvaro B. Onofrio
    The title compound (with the systematic name 2-{[(1S)-1-(methoxy­carbonyl)-3-methyl­butyl]amino­carbonyl}benzoic acid), C15H19NO5, crystallizes in the monoclinic space group P21, with two independent mol­ecules per asymmetric unit. The most notable difference between the two mol­ecules is in the dihedral angles between the planes of the carboxyl group and the benzene ring, which are 3.5,(3) and 25.7,(1)°. This difference may account for the fact that two competing reactions are observed in aqueous solution, namely cyclization to form the imide N -phthaloyl­leucine and hydrolysis of N -(2-carboxy­benzoyl)- l -leucine methyl ester to phthalic acid and leucine. [source]

    Two new non-centrosymmetric lithium salts of glycine: bis(glycine) lithium chromate monohydrate and bis(glycine) lithium molybdate

    Michel Fleck
    In bis­(glycine) lithium chromate monohydrate {systematic name: poly[aquadi-,-glycinato-,-tetra­oxochromato(VI)-dilithium(I)]}, [CrLi2(C2H5NO2)2O4(H2O)]n, (I) (space group P212121), and bis­(glycine) lithium molybdate {systematic name: poly[di-,-glycinato-,-tetra­oxomolybdato(VI)-dilithium(I)]}, [Li2Mo(C2H5NO2)2O4]n, (II) (space group P21), all atoms are located on general positions. The crystal structure of (I) is characterized by infinite chains of corner-sharing [LiO4] tetra­hedra, which are connected by glycine mol­ecules to form layers. [CrO4] tetra­hedra are attached to the [LiO4] tetra­hedra. Compound (II) contains dimers of [LiO4] tetra­hedra which are connected by [MoO4] tetra­hedra to form chains, which are in turn connected by glycine mol­ecules to form double layers. [source]

    Structure of the Escherichia coli RNA polymerase , subunit C-terminal domain

    Samuel Lara-González
    The , subunit C-terminal domain (,CTD) of RNA polymerase (RNAP) is a key element in transcription activation in Escherichia coli, possessing determinants responsible for the interaction of RNAP with DNA and with transcription factors. Here, the crystal structure of E. coli,CTD (, subunit residues 245,329) determined to 2.0,Å resolution is reported. Crystals were obtained after reductive methylation of the recombinantly expressed domain. The crystals belonged to space group P21 and possessed both pseudo-translational symmetry and pseudo-merohedral twinning. The refined coordinate model (R factor = 0.193, Rfree = 0.236) has improved geometry compared with prior lower resolution determinations of the ,CTD structure [Jeon et al. (1995), Science, 270, 1495,1497; Benoff et al. (2002), Science, 297, 1562,1566]. An extensive dimerization interface formed primarily by N- and C-terminal residues is also observed. The new coordinates will facilitate the improved modeling of ,CTD-containing multi-component complexes visualized at lower resolution using X-ray crystallography and electron-microscopy reconstruction. [source]

    Two crystal modifications of (Pro-Pro-Gly)4 -Hyp-Hyp-Gly-(Pro-Pro-Gly)4 reveal the puckering preference of Hyp(X) in the Hyp(X):Hyp(Y) and Hyp(X):Pro(Y) stacking pairs in collagen helices

    Kenji Okuyama
    Two crystal modifications of a collagen model peptide, (Pro-Pro-Gly)4 -Hyp-Hyp-Gly-(Pro-Pro-Gly)4 [where Hyp is (4R,2S)- l -hydroxyproline], showed very similar unit-cell parameters and belonged to the same space group P21. Both crystals exhibited pseudo-merohedral twinning. The main difference was in their molecular-packing arrangements. One modification showed pseudo-hexagonal packing, while the other showed pseudo-tetragonal packing. Despite their different packing arrangements, no significant differences were observed in the hydration states of these modifications. The peptide in the pseudo-tetragonal crystal showed a cyclic fluctuation of helical twists with a period of 20,Å, while that in the pseudo-hexagonal crystal did not. In these modifications, the puckering conformations of four of the 12 Hyp residues at the X position of the Hyp(X)-Hyp(Y)-Gly sequence were in the opposite conformations to the previous hypothesis that Hyp(X) residues involved in Hyp(X):Hyp(Y) and Hyp(X):Pro(Y) stacking pairs prefer up-puckering and down-puckering conformations, respectively. Detailed investigation of the molecular interactions between Hyp(X) and adjacent molecules revealed that these opposite conformations appeared because the puckering conformation, which follows the hypothesis, is subject to steric hindrance from the adjacent molecule. [source]

    A case of structure determination using pseudosymmetry

    Sergei Radaev
    Here, a case is presented of an unusual structure determination which was facilitated by the use of pseudosymmetry. Group A streptococcus uses cysteine protease Mac-1 (also known as IdeS) to evade the host immune system. Native Mac-1 was crystallized in the orthorhombic space group P21212. Surprisingly, crystals of the inactive C94A mutant of Mac-1 displayed monoclinic symmetry with space group P21, despite the use of native orthorhombic Mac-1 microcrystals for seeding. Attempts to solve the structure of the C94A mutant by MAD phasing in the monoclinic space group did not produce an interpretable map. The native Patterson map of the C94A mutant showed two strong peaks along the (1 0 1) diagonal, indicating possible translational pseudosymmetry in space group P21. Interestingly, one-third of the monoclinic reflections obeyed pseudo-orthorhombic P21212 symmetry similar to that of the wild-type crystals and could be indexed and processed in this space group. The pseudo-orthorhombic and monoclinic unit cells were related by the following vector operations: am = bo,co, bm = ao and cm = ,2co,bo. The pseudo-orthorhombic subset of data produced good SAD phases, leading to structure determination with one monomer in the asymmetric unit. Subsequently, the structure of the Mac-1 mutant in the monoclinic form was determined by molecular replacement, which showed six molecules forming three translationally related dimers aligned along the (1 0 1) diagonal. Knowing the geometric relationship between the pseudo-orthorhombic and the monoclinic unit cells, all six molecules can be generated in the monoclinic unit cell directly without the use of molecular replacement. The current case provides a successful example of the use of pseudosymmetry as a powerful phase-averaging method for structure determination by anomalous diffraction techniques. In particular, a structure can be solved in a higher pseudosymmetry subcell in which an NCS operator becomes a crystallographic operator. The geometrical relationships between the subcell and parental cell can be used to generate a complete molecular representation of the parental asymmetric unit for refinement. [source]

    A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity

    Daniel A. Breustedt
    Tear lipocalin (TLC) with the bound artificial ligand 1,4-butanediol has been crystallized in space group P21 with four protein molecules in the asymmetric unit and its X-ray structure has been solved at 2.6,Å resolution. TLC is a member of the lipocalin family that binds ligands with diverse chemical structures, such as fatty acids, phospholipids and cholesterol as well as microbial siderophores and the antibiotic rifampin. Previous X-ray structural analysis of apo TLC crystallized in space group C2 revealed a rather large bifurcated ligand pocket and a partially disordered loop region at the entrace to the cavity. Analysis of the P21 crystal form uncovered major conformational changes (i) in ,-strands B, C and D, (ii) in loops 1, 2 and 4 at the open end of the ,-barrel and (iii) in the extended C-terminal segment, which is attached to the ,-barrel via a disulfide bridge. The structural comparison indicates high conformational plasticity of the loop region as well as of deeper parts of the ligand pocket, thus allowing adaptation to ligands that differ vastly in size and shape. This illustrates a mechanism for promiscuity in ligand recognition which may also be relevant for some other physiologically important members of the lipocalin protein family. [source]

    Imperfect pseudo-merohedral twinning in crystals of fungal fatty acid synthase

    Simon Jenni
    The recent high-resolution structures of fungal fatty acid synthase (FAS) have provided new insights into the principles of fatty acid biosynthesis by large multifunctional enzymes. The crystallographic phase problem for the 2.6,MDa fungal FAS was initially solved to 5,Å resolution using two crystal forms from Thermomyces lanuginosus. Monoclinic crystals in space group P21 were obtained from orthorhombic crystals in space group P212121 by dehydration. Here, it is shown how this space-group transition induced imperfect pseudo-merohedral twinning in the monoclinic crystal, giving rise to a Moiré pattern-like interference of the two twin-related reciprocal lattices. The strategy for processing the twinned diffraction images and obtaining a quantitative analysis is presented. The twinning is also related to the packing of the molecules in the two crystal forms, which was derived from self-rotation function analysis and molecular-replacement solutions using a low-resolution electron microscopy map as a search model. [source]

    Structure of a d(TGGGGT) quadruplex crystallized in the presence of Li+ ions

    Christophe Creze
    A parallel 5,-d(TGGGGT)-3, quadruplex was formed in Na+ solution and crystallized using lithium sulfate as the main precipitating agent. The X-ray structure was determined to 1.5,Å resolution in space group P21 by molecular replacement. The asymmetric unit consists of a characteristic motif of two quadruplexes stacked at their 5, ends. All nucleotides are clearly defined in the density and could be positioned. A single bound Li+ ion is observed at the surface of the column formed by the two joined molecules. Thus, this small alkali metal ion appears to be unsuitable as a replacement for the Na+ ion in the central channel of G-quartets, unlike K+ or Tl+ ions. A well conserved constellation of water molecules is observed in the grooves of the dimeric structure. [source]

    Structure of a pseudomerohedrally twinned monoclinic crystal form of a pyridoxal phosphate-dependent catalytic antibody

    Béatrice Golinelli-Pimpaneau
    The purification, crystallization and structure determination at 2.3,Å resolution of the complex of the pyridoxal-5,-phosphate (PLP) dependent catalytic antibody 15A9 with a phosphopyridoxyl- l -alanine (PPL- l -alanine) substrate analogue are described. The crystal belongs to space group P21, with two molecules in the asymmetric unit related by non-crystallographic symmetry. The unit-cell parameters are a = 63.5, b = 81.7, c = 79.3,Å and , is fortuitously 90°. Refinement of the structure converged at unacceptably high R factors. Although the traditional analysis of intensity distribution did not indicate twinning, pseudomerohedral twinning was revealed by a newer test based on local intensity differences [Padilla & Yeates (2003), Acta Cryst. D59, 1124,1130]. When the potential twinning operator was included in SHELX, the structure could be satisfactorily refined with a twinning fraction of 0.46, indicating a nearly perfect hemihedrally twinned crystal. One of the active sites is occupied by the phosphopyridoxyl- l -alanine ligand, while one iodide ion mimics the cofactor phosphate group in the other. Four other iodide ions are present in the structure: two are involved in specific intermolecular contacts and two dictate the conformation of the CDRH3 loop in each molecule. [source]

    Expression, crystallization and preliminary X-ray crystallographic studies of Klebsiella pneumoniae maltohexaose-producing ,-amylase

    Mitsuru Momma
    A recombinant form of Klebsiella pneumoniae maltohexaose-producing ,-amylase has been overexpressed in Escherichia coli and purified to homogeneity. Crystals were obtained at 293,K by the microbatch technique using 80,mM sodium/potassium phosphate buffer pH 6.2 containing 8% polyethylene glycol 3000, 4% polyethylene glycol 3350 and 40,mM sodium thiocyanate. Crystals of the overexpressed recombinant enzyme diffracted to better than 2.5,Å resolution at 95,K using a synchrotron-radiation source. The crystals belong to the primitive monoclinic space group P21, with unit-cell parameters a = 74.8, b = 107.6, c = 82.2,Å, , = 96.2°. Assuming the presence of two molecules per asymmetric unit, the VM value for the crystal was 2.3,Å3,Da,1, indicating a solvent content of 47%. [source]

    Crystallization and preliminary X-ray crystallographic analysis of the laminarinase endo-,-1,3-glucanase from Pyrococcus furiosus

    Andrea Ilari
    Laminarinase endo-,-1,3 glucanase (LamA) from Pyrococcus furiosus is an enzyme which displays its main hydrolytic activity on the ,-1,3-glucose polymer laminarin. This laminarinase is remarkably resistant to denaturation: its secondary structure is unchanged in 8,M guanidinium chloride. This protein belongs to the family 16 glycosyl hydrolases, which are enzymes that are widely distributed among bacteria, fungi and higher plants. Single crystals of P. furiosus LamA have been obtained by the hanging-drop vapour-diffusion method using 2-­methyl-2,4-pentanediol as a precipitant agent. A complete data set has been collected under cryocooling at a synchrotron source. The crystals belong to the monoclinic space group P21, with unit-cell parameters a = 44.36, b = 84.76, c = 69.23,Å, , = 90, , = 104.97, , = 90°, and diffract to 2.15,Å resolution. [source]

    Crystallization and preliminary X-ray crystallographic studies of mouse autocrine motility factor

    Noriko Naba
    Mouse autocrine motility factor (mAMF), a tumour-secreted cytokine that stimulates cell migration in vitro and metastasis in vivo, has been crystallized by the hanging-drop vapour-diffusion method. The crystals belong to the monoclinic space group P21, with unit-cell parameters a = 69.97, b = 115.88, c = 73.27,Å, , = 101.76°. There are two subunits (one dimer) per asymmetric unit. Complexes with four-, five- and six-carbon carbohydrate phosphate inhibitors have also been crystallized. The crystals diffract to at least 1.8,Å resolution and are suitable for X-ray structure analyses at high resolution. [source]

    Crystallization and preliminary X-ray analysis of cellobiose phosphorylase from Cellvibrio gilvus

    Masafumi Hidaka
    A recombinant cellobiose phosphorylase from Cellvibrio gilvus has been prepared and crystallized by the sitting-drop vapour-diffusion method using 10,mg,ml,1 purified enzyme, 1.5,M ammonium sulfate, 0.1,M MES buffer pH 7.0 and 5,mM glucose. A suitable crystal was obtained after 10,d incubation at 298,K. The crystal belongs to space group P21, with unit-cell parameters a = 84.77, b = 98.31, c = 104.04,Å, , = 102.73°. X-ray diffraction data to 2.1,Å resolution have been collected at KEK-PF BL-5A. [source]

    Crystallization and preliminary X-ray analysis of a C-terminal TonB fragment from Escherichia coli

    Jiri Koedding
    The TonB protein located in the cell wall of Gram-negative bacteria mediates the proton motive force from the cytoplasmic membrane to specific outer membrane transporters. A C-terminal fragment of TonB from Escherichia coli consisting of amino-acid residues 147,239 (TonB-92) has been purified and crystallized. Crystals grew in space group P21 to dimensions of about 1.0 × 0.12 × 0.12,mm. A native data set has been obtained to 1.09,Å resolution. [source]

    Crystallization and preliminary crystallographic studies of the D59A mutant of MicA, a YycF response-regulator homologue from Streptococcus pneumoniae

    Alan Riboldi-Tunnicliffe
    RR02 (MicA) is an essential bacterial protein that belongs to the YycF family of response regulators and consists of two domains: an N-­terminal receiver domain and a C-terminal effector domain. Streptococcus pneumoniae RR02 (MicA; residues 2,234) has been crystallized using the sitting-drop vapour-diffusion technique. The crystals belong to space group P21, with unit-cell parameters a = 46.46, b = 32.61, c = 63.35,Å, , = 90.01°. X-ray diffraction data have been collected to 1.93,Å resolution. [source]

    Crystallization and preliminary X-ray crystallographic analyses of CMY-1 and CMY-10, plasmidic class C ,-lactamases with extended substrate spectrum

    Sun-Joo Lee
    Plasmid-encoded class C ,-lactamases, including CMY-1 and CMY-­10, hydrolyze the lactam bonds of ,-lactam antibiotics, inducing therapeutic failure and a lack of eradication of clinical isolates by third-generation cephalosporins or cephamycins. Therefore, the enzymes are potential targets for developing agents against pathogens isolated from patients suffering from wound infection, urinary tract infection or pneumonia. CMY-1 and CMY-10 were purified and crystallized at 298,K. X-ray diffraction data from CMY-1 and CMY-­10 crystals have been collected to 2.5 and 1.5,Å resolution, respectively, using synchrotron radiation. The crystals of the two proteins are isomorphous and belong to the primitive monoclinic space group P21. [source]

    Co-crystallization of Leptospira interrogans peptide deformylase with a potent inhibitor and molecular-replacement schemes with eight subunits in an asymmetric unit

    Peptide deformylase
    Translation initiation in eubacteria involves a formylmethionine at the N-terminus of newly synthesized polypeptides. This N-formyl group is removed by peptide deformylase (PDF) during the post-translation process. Such a formylation/deformylation cycle is essential for the cell survival of eubacteria, but is not utilized in eukaryotic cytosolic protein biosynthesis. In view of the absence of deformylase activity in mammalian cells, this is an attractive target for the design of novel antibiotic drugs. Co-crystallization of peptide deformylase from Leptospira interrogans (LiPDF) with its natural inhibitor actinonin produced diffraction-quality crystals that belong to space group P21, with unit-cell parameters a = 87.5, b = 119.1, c = 95.8,Å, , = 111.6°. The 3.1,Å resolution data set collected in-house was used to obtain phases by molecular replacement. Three schemes for the correction of the preliminary solutions were proposed and proved successful in determining the structure of LiPDF with eight subunits in the asymmetric unit. [source]

    Crystallization, preliminary X-ray analysis and molecular-replacement solution of haemoglobin-II from the fish matrinxã (Brycon cephalus)

    J. C. L. Fonseca
    Haemoglobins constitute a set of proteins with interesting structural and functional properties, especially when the two large animal groups reptiles and fishes are focused on. Here, the crystallization and preliminary X-ray analysis of haemoglobin-II from the South American fish matrinxã (Brycon cephalus) is reported. X-ray diffraction data have been collected to 3.0,Å resolution using synchrotron radiation (LNLS). Crystals were determined to belong to space group P21 and preliminary structural analysis revealed the presence of two tetramers in the asymmetric unit. The structure was determined using the standard molecular-replacement technique. [source]

    Purification, crystallization and preliminary X-ray analysis of the Enterococcus faecalis protein EF0377

    Alan Riboldi-Tunnicliffe
    The EF0377 gene of Enterococcus faecalis was cloned and overexpressed in Escherichia coli. The protein has been purified and crystallized in three forms. Type III crystals belong to space group P21, with unit-cell parameters a = 72.11, b = 94.97, c = 80.77,Å, , = 111.93°. There are four molecules per asymmetric unit and diffraction is observed to beyond 1.65,Å under cryoconditions (100,K) using synchrotron radiation. An almost complete set of X-­ray diffraction data was collected to 1.9,Å from the native crystal. [source]

    Structural comparison of Escherichia colil -asparaginase in two monoclinic space groups

    Mario Sanches
    The functional l -asparaginase from Escherichia coli is a homotetramer with a molecular weight of about 142,kDa. The X-ray structure of the enzyme, crystallized in a new form (space group C2) and refined to 1.95,Å resolution, is compared with that of the previously determined crystal form (space group P21). The asymmetric unit of the new crystal form contains an l -asparaginase dimer instead of the tetramer found in the previous crystal form. It is found that crystal contacts practically do not affect the conformation of the protein. It is shown that subunit C of the tetrameric form is in a conformation which is systematically different from that of all other subunits in both crystal forms. Major conformational differences are confined to the lid loop (residues 14,27). In addition, the stability of this globular protein is analyzed in terms of the interactions between hydrophobic parts of the subunits. [source]