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Crystallographic Asymmetric Unit (crystallographic + asymmetric_unit)
Selected AbstractsEfficient 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 AgentsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 6 2007Joaquín 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] Crystal structure of a dimeric form of streptococcal pyrogenic exotoxin A (SpeA1)PROTEIN SCIENCE, Issue 9 2004Matthew 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 recognitionPROTEIN SCIENCE, Issue 6 2001Matthew 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] Emerging from pseudo-symmetry: the redetermination of human carbonic anhydrase II in monoclinic P21 with a doubled a axisACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2010Arthur H. Robbins The crystal structure of human carbonic anhydrase II in the monoclinic P21 space group with a doubled a axis from that of the usually observed unit cell has recently been reported, with one of the two molecules in the asymmetric unit demonstrating rotational disorder [Robbins et al. (2010), Acta Cryst. D66, 628,634]. The structure has been redetermined, with the coordinates of both pseudo-symmetrically related molecules in the crystallographic asymmetric unit translated by x, = x± 1/4, and no rotational disorder is observed. This corresponds to a different choice of how the four molecules in the unit cell should be grouped into pairs that represent a single asymmetric unit. [source] The high-resolution structure of pig heart succinyl-CoA:3-oxoacid coenzyme A transferaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2010Shu-Fen Coker The enzyme succinyl-CoA:3-oxoacid coenzyme A transferase (SCOT) participates in the metabolism of ketone bodies in extrahepatic tissues. It catalyses the transfer of coenzyme A (CoA) from succinyl-CoA to acetoacetate with a classical ping-pong mechanism. There is biochemical evidence that the enzyme undergoes conformational changes during the reaction, but no domain movements have been reported in the available crystal structures. Here, a structure of pig heart SCOT refined at 1.5,Å resolution is presented, showing that one of the four enzyme subunits in the crystallographic asymmetric unit has a molecule of glycerol bound in the active site; the glycerol molecule is hydrogen bonded to the conserved catalytic glutamate residue and is likely to occupy the cosubstrate-binding site. The binding of glycerol is associated with a substantial relative movement (a 13° rotation) of two previously undefined domains that close around the substrate-binding site. The binding orientation of one of the cosubstrates, acetoacetate, is suggested based on the glycerol binding and the possibility that this dynamic domain movement is of functional importance is discussed. [source] Structure of laminin-binding adhesin (Lmb) from Streptococcus agalactiaeACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2009Preethi Ragunathan Adhesion/invasion of pathogenic bacteria is a critical step in infection and is mediated by surface-exposed proteins termed adhesins. The crystal structure of recombinant Lmb, a laminin-binding adhesin from Streptococcus agalactiae, has been determined at 2.5,Å resolution. Based on sequence and structural homology, Lmb was placed into the cluster 9 family of the ABC (ATP-binding cassette) transport system. The structural organization of Lmb closely resembles that of ABC-type solute-binding proteins (SBPs), in which two structurally related globular domains interact with each other to form a metal-binding cavity at the interface. The bound zinc in Lmb is tetrahedrally coordinated by three histidines and a glutamate from both domains. A comparison of Lmb with other metal transporters revealed an interesting feature of the dimerization of molecules in the crystallographic asymmetric unit in all zinc-binding transporters. A closer comparison of Lmb with the zinc-binding ZnuA from Escherichia coli and Synechocystis 6803 suggested that Lmb might undergo a unique structural rearrangement upon metal binding and release. The crystal structure of Lmb provides an impetus for further investigations into the molecular basis of laminin binding by human pathogens. Being ubiquitous in all serotypes of group B streptococcus (GBS), the structure of Lmb may direct the development of an efficient vaccine. [source] Crystallization and preliminary X-ray crystallographic analysis of a non-specific lipid-transfer protein with antipathogenic activity from Phaseolus mungoACTA CRYSTALLOGRAPHICA SECTION D, Issue 12-2 2004Shao-Yun Wang A 9,kDa non-specific lipid-transfer protein (nsLTP) from mung bean (Phaseolus mungo) seeds, displaying antifungal activity, antibacterial activity and lipid-transfer activity, was crystallized at 297,K using ammonium sulfate as a precipitant by means of the hanging-drop vapour-diffusion method. Native X-ray diffraction data were collected to a resolution of 2.4,Å. The crystals are rhombohedral, belonging to space group P212121, with unit-cell parameters a = 38.671, b = 51.785, c = 55.925,Å. Assuming the presence of one molecule in the crystallographic asymmetric unit results in a Matthews coefficient (VM) of approximately 3.0,Å3,Da,1, corresponding to a solvent content of about 58%. [source] Structure of d -ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2004Eric L. Wise The crystal structure of d -ribulose 5-phosphate 3-epimerase (RPE) from the cyanobacterium Synechocystis was determined by X-ray crystallography to 1.6,Å resolution. The enzyme, which catalyzes the epimerization of d -ribulose 5-phosphate and d -xylulose 5-phosphate, assembles as a hexamer of (,/,)8 -barrels in the crystallographic asymmetric unit. The active site is highly similar to those of two previously reported RPEs and provides further evidence for essential catalytic roles for several active-site residues. [source] A novel method of determining the number of macromolecules per asymmetric unit from accurate crystal-volume measurementsACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2003Fang Li Knowledge of the number of macromolecules per crystallographic asymmetric unit is frequently useful in the determination of crystal structures. A method has been developed to establish this number directly from measurements of the volume and macromolecular contents of a crystal. The volume of a crystal is determined by measuring the volume of solvent that it displaces in a fine capillary tube. The macromolecular mass contained in a crystal is measured by dissolving the crystal in a known amount of water or suitable buffer and then measuring the UV absorbance of the solution. The method has been tested successfully on three different crystals of known structures. [source] Structure of pteridine reductase (PTR1) from Leishmania tarentolaeACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2003Haiyan Zhao The protozoan parasites Leishmania utilize a pteridine-reducing enzyme, pteridine reductase (PTR1), to bypass antifolate inhibition. The crystal structure of PTR1 from L. tarentolae has been solved as a binary complex with NADPH at 2.8,Å resolution. The structure was solved by molecular-replacement techniques using the recently reported L. major PTR1 structure as a search model. Comparisons of the present structure with the L. major PTR1 allowed us to identify regions of flexibility in the molecule. PTR1 is a member of the growing family of short-chain dehydrogenases (SDR) which share the characteristic Tyr(Xaa)3Lys motif in the vicinity of the active site. The functional enzyme is a tetramer and the crystallographic asymmetric unit contains a tetramer with 222 point-group symmetry. [source] Crystallization and preliminary X-ray analysis of bucain, a novel toxin from the Malayan krait Bungarus candidusACTA CRYSTALLOGRAPHICA SECTION D, Issue 10-2 2002L. Watanabe Bucain is a three-finger toxin, structurally homologous to snake-venom muscarinic toxins, from the venom of the Malayan krait Bungarus candidus. These proteins have molecular masses of approximately 6000,8000,Da and encompass the potent curaremimetic neurotoxins which confer lethality to Elapidae and Hydrophidae venoms. Bucain was crystallized in two crystal forms by the hanging-drop vapour-diffusion technique in 0.1,M sodium citrate pH 5.6, 15% PEG 4000 and 0.15,M ammonium acetate. Form I crystals belong to the monoclinic system space group C2, with unit-cell parameters a = 93.73, b = 49.02, c = 74.09,Å, , = 111.32°, and diffract to a nominal resolution of 1.61,Å. Form II crystals also belong to the space group C2, with unit-cell parameters a = 165.04, b = 49.44, c = 127.60,Å, , = 125.55°, and diffract to a nominal resolution of 2.78,Å. The self-rotation function indicates the presence of four and eight molecules in the crystallographic asymmetric unit of the form I and form II crystals, respectively. Attempts to solve these structures by molecular-replacement methods have not been successful and a heavy-atom derivative search has been initiated. [source] Structure of lobster apocrustacyanin A1 using softer X-raysACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2001M. Cianci The molecular basis of the camouflage colouration of marine crustacea is often provided by carotenoproteins. The blue colour of the lobster carapace, for example, is intricately associated with a multimacromolecular 16-mer complex of protein subunits each with a bound astaxanthin molecule. The protein subunits of crustacyanin fall into two distinct subfamilies, CRTC and CRTA. Here, the crystal structure solution of the A1 protein of the CRTC subfamily is reported. The problematic nature of the structure solution of the CRTC proteins (both C1 and A1) warranted consideration and the development of new approaches. Three putative disulfides per protein subunit were likely to exist based on molecular-homology modelling against known lipocalin protein structures. With two such subunits per crystallographic asymmetric unit, this direct approach was still difficult as it involved detecting a weak signal from these sulfurs and suggested the use of softer X-rays, combined with high data multiplicity, as reported previously [Chayen et al. (2000), Acta Cryst. D56, 1064,1066]. This paper now describes the structure solution of CRTC in the form of the A1 dimer based on use of softer X-rays (2,Å wavelength). The structure solution involved a xenon derivative with an optimized xenon LI edge signal and a native data set. The hand of the xenon SIROAS phases was determined by using the sulfur anomalous signal from a high-multiplicity native data set also recorded at 2,Å wavelength. For refinement, a high-resolution data set was measured at short wavelength. All four data sets were collected at 100,K. The refined structure to 1.4,Å resolution based on 60,276 reflections has an R factor of 17.7% and an Rfree of 22.9% (3137 reflections). The structure is that of a typical lipocalin, being closely related to insecticyanin, to bilin-binding protein and to retinol-binding protein. This A1 monomer or dimer can now be used as a search motif in the structural studies of the oligomeric forms ,- and ,-crustacyanins, which contain bound astaxanthin molecules. [source] Crystallization and preliminary crystallographic studies of RhoGDI in complex with the radixin FERM domainACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2001Keisuke Hamada The Rho guanine nucleotide-dissociation inhibitor (RhoGDI) is a general regulator that forms a complex with the GDP-bound form of Rho-family GTPases and suppresses their activation. The FERM domains of ERM (ezrin/radixin/moesin) proteins bind to RhoGDI and dissociate Rho from RhoGDI. The formation of a complex between RhoGDI and the FERM domain is an important step in the regulatory cycle of Rho activation. In this study, crystals of RhoGDI complexed with the FERM domain of radixin were obtained. The crystals of the binary complex belong to the space group P21212, with unit-cell parameters a = 130.9,(2), b = 151.2,(2), c = 71.2,(1),Å, and contain two protein complexes in the crystallographic asymmetric unit. A 2.9,Å resolution data set was collected using synchrotron radiation at SPring-8. [source] Crystallographic characterization of the radixin FERM domain bound to the cytoplasmic tail of the adhesion protein ICAM-2ACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2001Keisuke Hamada Radixin is a member of the ERM proteins, which cross-link plasma membranes and actin filaments. The FERM domains located at the N-terminal regions of ERM proteins are responsible for membrane association through direct interactions with the cytoplasmic domains of integral membrane proteins. Here, crystals of the complex between the radixin FERM domain and the full-length cytoplasmic tail (28-residue peptide) of intercellular adhesion molecule 2, ICAM-2, have been obtained. The crystals were found to belong to space group P3121 or P3221, with unit-cell parameters a = b = 100.44,(9), c = 99.49,(6),Å, and contain one complex in the crystallographic asymmetric unit. An intensity data set was collected to a resolution of 2.60,Å. [source] Crystallization and preliminary X-ray analysis of eukaryotic initiation factor 4E from Pisum sativumACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Jamie A. Ashby Crystals of an N-terminally truncated 20,kDa fragment of Pisum sativum eIF4E (,N-eIF4E) were grown by vapour diffusion. X-ray data were recorded to a resolution of 2.2,Å from a single crystal in-house. Indexing was consistent with primitive monoclinic symmetry and solvent-content estimations suggested that between four and nine copies of the eIF4E fragment were possible per crystallographic asymmetric unit. eIF4E is an essential component of the eukaryotic translation machinery and recent studies have shown that point mutations of plant eIF4Es can confer resistance to potyvirus infection. [source] Site-specific unglycosylation to improve crystallization of the metabotropic glutamate receptor 3 extracellular domainACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2009Takanori Muto Metabotropic glutamate receptors (mGluRs) are involved in the regulation of many physiological and pathological processes in the central nervous system. The extracellular domain (ECD) of mGluR subtype 3 (mGluR3) was produced using the baculovirus expression system and purified from the culture medium. However, the recombinant protein showed heterogeneity in molecular weight on SDS,PAGE analysis. It was found that the unglycosylation of Asn414 significantly reduced the heterogeneity. Consequently, three site-specifically unglycosylated mutant proteins of mGluR3 ECD, replacing Asn414 only or replacing Asn414 in combination with other glycosylation sites, were successfully crystallized in the presence of l -glutamate. Among them, crystals of the N414/439Q mutant diffracted X-rays to 2.35,Å resolution using synchrotron radiation. The crystal belonged to the monoclinic space group P21, with unit-cell parameters a = 84.0, b = 97.5, c = 108.1,Å, , = 93.0°. Assuming the presence of two protomers per crystallographic asymmetric unit, the Matthews coefficient VM was calculated to be 3.5,Å3,Da,1 and the solvent content was 65%. [source] Expression, purification, crystallization and preliminary X-ray analysis of the ligand-binding domain of metabotropic glutamate receptor 7ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2007Takanori Muto Glutamate is the major excitatory neurotransmitter and its metabotropic glutamate receptor (mGluR) plays an important role in the central nervous system. The ligand-binding domain (LBD) of mGluR subtype 7 (mGluR7) was produced using the baculovirus expression system and purified from the culture medium. The purified protein was characterized by gel-filtration chromatography, SDS,PAGE and a ligand-binding assay. Crystals of mGluR7 LBD were grown at 293,K by the hanging-drop vapour-diffusion method. The crystals diffracted X-rays to 3.30,Å resolution using synchrotron radiation and belong to the trigonal space group P3121, with unit-cell parameters a = b = 92.4, c = 114.3,Å. Assuming the presence of one protomer per crystallographic asymmetric unit, the Matthews coefficient VM was calculated to be 2.5,Å3,Da,1 and the solvent content was 51%. [source] Crystallographic characterization of the radixin FERM domain bound to the cytoplasmic tails of adhesion molecules CD43 and PSGL-1ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2007Yumiko Takai Radixin is a member of the ERM proteins that cross-link plasma membranes and actin filaments. The FERM domains located in the N-terminal regions of ERM proteins are responsible for membrane association through direct interaction with the cytoplasmic tails of integral membrane proteins. Here, crystals of the radixin FERM domain bound to the cytoplasmic peptides of two adhesion molecules, CD43 and PSGL-1, have been obtained. Crystals of the radixin FERM domain bound to CD43 belong to space group P4322, with unit-cell parameters a = b = 68.72, c = 201.39,Å, and contain one complex in the crystallographic asymmetric unit. Crystals of the radixin FERM domain bound to PSGL-1 belong to space group P212121, with unit-cell parameters a = 80.74, b = 85.73, c = 117.75,Å, and contain two complexes in the crystallographic asymmetric unit. Intensity data sets were collected to a resolution of 2.9,Å for the FERM,CD43 complex and 2.8,Å for the FERM,PSGL-1 complex. [source] | ||||||||||