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Space Group P3121 (space + group_p3121)
Kinds of Space Group P3121 Selected AbstractsMicrostructure of a Complex Oxide, Ho2MnxTa2,xO7(x, 1.0), with a Pyrochlore-Related StructureJOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 9 2000Hiromi Nakano The ternary compound Ho2MnxTa2,xO7 was synthesized in air at 1523 K. Structural characterization of the compound was taken by X-ray diffractometry (XRD) and transmission electron microscopy (TEM). The compound possessed a trigonal super cell derived from a rhombohedral basic cell with the a/2 of the trigonal super cell. The super cell was caused by the ordering of Mn and Ta ions and the derived structure model was in agreement with that of the zirkelite structure with the space group P3121. The compound had stacking disorder with different stacking sequences along the c -axis. An orientation anomaly in the super cell reflections revealed that the super cell had an incommensurate nature. [source] Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxinACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009Megan Guelker The crystal structure of oxidized flavodoxin from Desulfovibrio desulfuricans (ATCC 29577) was determined by molecular replacement in two crystal forms, P3121 and P43, at 2.5 and 2.0,Å resolution, respectively. Structure determination in space group P3121 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8). Initial phasing attempts in space group P3121 by molecular replacement using a poor search model (46% identity) and multi-wavelength anomalous dispersion were unsuccessful. It was necessary to solve the structure in a second crystal form, space group P43, which was characterized by almost perfect twinning, in order to obtain a suitable search model for molecular replacement. This search model with complementary approaches to molecular replacement utilizing the pseudo-translational symmetry operators determined by analysis of the native Patterson map facilitated the selection and manual placement of molecules to generate an initial solution in the P3121 crystal form. During the early stages of refinement, application of the appropriate twin law, (,h, ,k, l), was required to converge to reasonable R -factor values despite the fact that in the final analysis the data were untwinned and the twin law could subsequently be removed. The approaches used in structure determination and refinement may be applicable to other crystal structures characterized by these complicating factors. The refined model shows flexibility of the flavin mononucleotide coordinating loops indicated by the isolation of two loop conformations and provides a starting point for the elucidation of the mechanism used for protein-partner recognition. [source] Structure of the inactive variant C60S of Mycobacterium tuberculosis thiol peroxidaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2006Matthias Stehr The genome of Mycobacterium tuberculosis encodes several peroxiredoxins (Prxs) thought to be active against organic and inorganic peroxides. The open reading frame Rv1932 encodes a 165-residue thiol peroxidase (Tpx), which belongs to the atypical 2-Cys peroxiredoxin family. The crystal structure of the C60S mutant of M. tuberculosis Tpx (MtTpx) crystallized in space group P3121, with unit-cell parameters a = 106.08, b = 106.08, c = 65.33,Å. The structure has been refined to an R value of 17.1% (Rfree = 24.9%) at 2.1,Å resolution. MtTpx is structurally homologous to other peroxiredoxins, including the mycobacterial AhpC and AhpE. The inactive MtTpx C60S mutant structure closely resembles the structure of Streptococcus pneumoniae Tpx (SpTpx) and thus represents the reduced enzyme state. The mutated active-site serine is electrostatically linked to Arg130 and hydrogen bonded to Thr57, practically identical to the cysteine in SpTpx. A cocrystallized acetate molecule mimics the position of the substrate and interacts with Ser60, Arg130 and Thr57. [source] Structure of pyrR (Rv1379) from Mycobacterium tuberculosis: a persistence gene and protein drug targetACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2005Katherine A. Kantardjieff The Mycobacterium tuberculosis pyrR gene (Rv1379) encodes a protein that regulates the expression of pyrimidine-nucleotide biosynthesis (pyr) genes in a UMP-dependent manner. Because pyrimidine biosynthesis is an essential step in the progression of TB, the gene product pyrR is an attractive antitubercular drug target. The 1.9,Å native structure of Mtb pyrR determined by the TB Structural Genomics Consortium facilities in trigonal space group P3121 is reported, with unit-cell parameters a = 66.64, c = 154.72,Å at 120,K and two molecules in the asymmetric unit. The three-dimensional structure and residual uracil phosphoribosyltransferase activity point to a common PRTase ancestor for pyrR. However, while PRPP- and UMP-binding sites have been retained in Mtb pyrR, a distinct dimer interaction among subunits creates a deep positively charged cleft capable of binding pyr mRNA. In silico screening of pyrimidine-nucleoside analogs has revealed a number of potential lead compounds that, if bound to Mtb pyrR, could facilitate transcriptional attenuation, particularly cyclopentenyl nucleosides. [source] Urate oxidase from Aspergillus flavus: new crystal-packing contacts in relation to the content of the active siteACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2005Pascal Retailleau Urate oxidase from Aspergillus flavus (uricase or Uox; EC 1.7.3.3) is a 135,kDa homotetramer with a subunit consisting of 301 amino acids. It catalyses the first step of the degradation of uric acid into allantoin. The structure of the extracted enzyme complexed with a purine-type inhibitor (8-azaxanthin) had been solved from high-resolution X-ray diffraction of I222 crystals. Expression of the recombinant enzyme in Saccharomyces cerevisiae followed by a new purification procedure allowed the crystallization of both unliganded and liganded enzymes utilizing the same conditions but in various crystal forms. Here, four different crystal forms of Uox are analyzed. The diversity of the Uox crystal forms appears to depend strongly on the chemicals used as inhibitors. In the presence of uracil and 5,6-diaminouracil crystals usually belong to the trigonal space group P3121, the asymmetric unit (AU) of which contains one tetramer of Uox (four subunits). Chemical oxidation of 5,6-diaminouracil within the protein may occur, leading to the canonical (I222) packing with one subunit per AU. Coexistence of two crystal forms, P21 with two tetramers per AU and I222, was found in the same crystallization drop containing another inhibitor, guanine. Finally, a fourth form, P21212 with one tetramer per AU, resulted fortuitously in the presence of cymelarsan, an additive. Of all the reported forms, the I222 crystal forms present by far the best X-ray diffraction resolution (,1.6,Å resolution compared with 2.3,3.2,Å for the other forms). The various structures and contacts in all crystalline lattices are compared. The backbones are essentially conserved except for the region near the active site. Its location at the dimer interface is thus likely to be at the origin of the crystal contact changes as a response to the various bound inhibitors. [source] Three-dimensional structural characterization of a novel Drosophila melanogaster acylphosphataseACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2004Simone Zuccotti Analysis of the Drosophila melanogaster EST database led to the discovery and cloning of a novel acylphosphatase. The CG18505 gene coding for a new enzyme (AcPDro2) is clearly distinct from the previously described CG16870Acyp gene, which also codes for a D. melanogaster acylphosphatase (AcPDro). The putative catalytic residues, together with residues held to stabilize the acylphosphatase fold, are conserved in the two encoded proteins. Crystals of AcPDro2, which belong to the trigonal space group P3121, with unit-cell parameters a = b = 45.8, c = 98.6,Å, , = 120°, allowed the solution of the protein structure by molecular replacement and its refinement to 1.5,Å resolution. The AcPDro2 active-site structure is discussed. [source] Crystallization, microPIXE and preliminary crystallographic analysis of the complex between the third KH domain of hnRNP K and single-stranded DNAACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2004Paul H. Backe hnRNP K is one of the major proteins found in hnRNP particles which are ribonucleoprotein complexes containing proteins and pre-mRNA. hnRNP K contains hnRNP K homology (KH) domains which bind both CT-rich single-stranded DNA (ssDNA) and CU-rich ssRNA. Co-crystallization of the third KH domain of human hnRNP,K with a 15-mer ssDNA gave rod-shaped crystals belonging to the trigonal space group P3121 (unit-cell parameters a = 54.0, c = 149.7,Å) and diffracting to 2.4,Å resolution. MicroPIXE (proton-induced X-ray emission) experiments showed that the crystals contained the complex and that the phosphorus to sulfur atomic ratio was consistent with the asymmetric unit containing three KH3 domains per 15-mer ssDNA. This was confirmed by structure solution by molecular replacement. [source] Crystallization and preliminary X-ray analysis of NADP(H)-dependent alcohol dehydrogenases from Saccharomyces cerevisiae and Rana pereziACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2003Eva Valencia Different crystal forms diffracting to high resolution have been obtained for two NADP(H)-dependent alcohol dehydrogenases, members of the medium-chain dehydrogenase/reductase superfamily: ScADHVI from Saccharomyces cerevisiae and ADH8 from Rana perezi. ScADHVI is a broad-specificity enzyme, with a sequence identity lower than 25% with respect to all other ADHs of known structure. The best crystals of ScADHVI diffracted beyond 2.8,Å resolution and belonged to the trigonal space group P3121 (or to its enantiomorph P3221), with unit-cell parameters a = b = 102.2, c = 149.7,Å, , = 120°. These crystals were produced by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. Packing considerations together with the self-rotation function and the native Patterson map seem to indicate the presence of only one subunit per asymmetric unit, with a volume solvent content of about 80%. ADH8 from R. perezi is the only NADP(H)-dependent ADH from vertebrates characterized to date. Crystals of ADH8 obtained both in the absence and in the presence of NADP+ using polyethylene glycol and lithium sulfate as precipitants diffracted to 2.2 and 1.8,Å, respectively, using synchrotron radiation. These crystals were isomorphous, space group C2, with approximate unit-cell parameters a = 122, b = 79, c = 91,Å, , = 113° and contain one dimer per asymmetric unit, with a volume solvent content of about 50%. [source] Structure of a complex of the potent and specific inhibitor BW284C51 with Torpedo californica acetylcholinesteraseACTA CRYSTALLOGRAPHICA SECTION D, Issue 10-2 2002Clifford E. Felder The X-ray crystal structure of Torpedo californica acetylcholinesterase (TcAChE) complexed with BW284C51 {CO[,CH2CH2,pC6H4,N(CH3)2(CH2,CH=CH2)]2} is described and compared with the complexes of two other active-site gorge-spanning inhibitors, decamethonium and E2020. The inhibitor was soaked into TcAChE crystals in the trigonal space group P3121, yielding a complex which diffracted to 2.85,Å resolution. The structure was refined to an R factor of 19.0% and an Rfree of 23.4%; the final model contains the protein, inhibitor, 132 water molecules and three carbohydrate moieties. BW284C51 binds similarly to decamethonium and E2020, with its two phenyl and quaternary amino end-groups complexed to Trp84 in the catalytic site and to Trp279 in the peripheral binding site, and its central carbonyl group hydrogen bonded very weakly to Tyr121. Possible reasons for decamethonium's weaker binding are considered. The relative strength of binding of bisquaternary inhibitors to acetylcholinesterase and the effect of several mutations of the enzyme are discussed in the context of the respective X-ray structures of their complexes with the enzyme. [source] Crystallization and preliminary X-ray crystallographic analysis of the Rv2002 gene product from Mycobacterium tuberculosis, a ,-ketoacyl carrier protein reductase homologueACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2002Jin Kuk Yang A 260-residue protein (FabG3) encoded by the Rv2002 gene of Mycobacterium tuberculosis shows amino-acid sequence similarity to ,-ketoacyl carrier protein (ACP) reductase, FabG. A soluble mutant (I6T/V47M/T69M) was produced by the green fluorescent protein-based directed-evolution method. It was crystallized at 296,K using the hanging-drop vapour-diffusion method. The diffraction quality of the crystal improved significantly after annealing/dehydration. X-ray diffraction data were collected to 1.8,Å resolution using synchrotron radiation. The crystal belongs to the space group P3121 (or P3221), with unit-cell parameters a = b = 70.38, c = 148.93,Å. The asymmetric unit contains two subunits, with a corresponding VM of 1.90,Å3,Da,1 and a solvent content of 35.3%. [source] Expression, crystallization and preliminary X-ray diffraction analysis of the CMM2 region of the Arabidopsis thaliana Morpheus' molecule 1 proteinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2010Tom J. Petty Of the known epigenetic control regulators found in plants, the Morpheus' molecule 1 (MOM1) protein is atypical in that the deletion of MOM1 does not affect the level of epigenetic marks controlling the transcriptional status of the genome. A short 197-amino-acid fragment of the MOM1 protein sequence can complement MOM1 deletion when coupled to a nuclear localization signal, suggesting that this region contains a functional domain that compensates for the loss of the full-length protein. Numerous constructs centred on the highly conserved MOM1 motif 2 (CMM2) present in these 197 residues have been generated and expressed in Escherichia coli. Following purification and crystallization screening, diamond-shaped single crystals were obtained that diffracted to ,3.2,Å resolution. They belonged to the trigonal space group P3121 (or P3221), with unit-cell parameters a = 85.64, c = 292.74,Å. Structure determination is ongoing. [source] Purification, crystallization and preliminary X-ray analysis of FliT, a bacterial flagellar substrate-specific export chaperoneACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Miki Kinoshita The assembly process of the bacterial flagellum is coupled to flagellar gene expression. FliT acts not only as a flagellar type III substrate-specific export chaperone for the filament-capping protein FliD but also as a negative regulator that suppresses flagellar gene expression through its specific interaction with the master regulator FlhD4C2 complex. In this study, FliT of Salmonella enterica serovar Typhimurium was expressed, purified and crystallized. Crystals of SeMet FliT were obtained by the sitting-drop vapour-diffusion technique with potassium/sodium tartrate as the precipitant. The crystals grew in the trigonal space group P3121 or P3221 and diffracted to 3.2,Å resolution. The anomalous difference Patterson map of the SeMet FliT crystal showed significant peaks in its Harker sections, indicating the usefulness of the derivative data for structure determination. [source] Purification, crystallization and preliminary X-ray analysis of the ,-lactamase Oih-1 from Oceanobacillus iheyensisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2009Marta Toth Bacterial resistance to the ,-lactam family of antibiotics is primarily the result of the deactivation of the drugs by ,-lactamase enzymes. The gene encoding the proficient ,-lactamase Oih-1 from the alkaliphilic and halotolerant Gram-positive bacterium Oceanobacillus iheyensis has been cloned and the mature wild-type protein (comprising 274 amino-acid residues) has been expressed in Escherichia coli and subsequently purified to homogeneity. Oih-1 crystallized in two crystal forms both belonging to the trigonal space group P3121 but with distinctly different unit-cell parameters. Synchrotron diffraction data were collected to high resolution (1.65,1.75,Å) from both crystal forms on beamlines BL7-1 and BL11-1 at SSRL (Stanford, California, USA). [source] Crystallization and preliminary X-ray analysis of carnein, a serine protease from Ipomoea carneaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2009Ashok Kumar Patel Carnein is an 80,kDa subtilisin-like serine protease from the latex of the plant Ipomoea carnea which displays an exceptional resistance to chemical and thermal denaturation. In order to obtain the first crystal structure of a plant subtilisin and to gain insight into the structural determinants underlying its remarkable stability, carnein was isolated from I. carnea latex, purified and crystallized by the hanging-drop vapour-diffusion method. A data set was collected to 2.0,Å resolution in-house from a single crystal at 110,K. The crystals belonged to the trigonal space group P3121 or P3221, with unit-cell parameters a = b = 126.9, c = 84.6,Å, , = , = 90, , = 120°. Assuming the presence of one molecule per asymmetric unit, the Matthews coefficient is 2.46,Å3,Da,1, corresponding to a solvent content of 50%. Structure determination of the enzyme is in progress. [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] Crystallization and preliminary X-ray characterization of aminopeptidase N from Escherichia coliACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2006Yuko Onohara A recombinant form of aminopeptidase N (molecular weight 99,kDa) from Escherichia coli was crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as a precipitating agent. The crystals belong to the hexagonal space group P3121, with unit-cell parameters a = b = 120.5, c = 171.0,Å. The crystals are most likely to contain one molecule in the asymmetric unit, with a VM value of 3.62,Å3,Da,1. Diffraction data were collected to 2.0,Å resolution using Cu,K, radiation from a rotating-anode X-ray generator. [source] Crystallization and preliminary X-ray diffraction studies on the catalytic domain of the chick retinal neurite-inhibitory factor CRYP-2ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2005T. S. Girish The receptor protein tyrosine phosphatase CRYP-2 has been shown to be an inhibitory factor for the growth of retinal axons in the chick. The extracellular receptor domain of CRYP-2 contains eight fibronectin repeats and studies using the extracellular domain alone demonstrated the chemorepulsive effect on retinal neurons. The precise role of the intracellular catalytic domain and the mechanism by which its activity is regulated is not known. Determination of the structure of the catalytic domain of CRYP-2 was proposed in an effort to understand the downstream signal transduction mechanism in this system. The cloning, expression, purification and crystallization of the catalytic domain of CRYP-2 are now reported. Preliminary crystallographic studies were performed on the diamond-shaped crystals, which grew under oil using the microbatch method at 298,K. Native X-ray diffraction data were collected to 2.9,Å resolution on a home source. The crystals belong to the trigonal space group P3121, with unit-cell parameters a = b = 68.26, c = 244.95,Å. Assuming the presence of two molecules per asymmetric unit, the VM value was 2.7,Å3,Da,1 and the solvent content was 54.8%. [source] | ||||||||||