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Group P41212 (group + p41212)
Kinds of Group P41212 Selected AbstractsStructure of a family 3b, carbohydrate-binding module from the Cel9V glycoside hydrolase from Clostridium thermocellum: structural diversity and implications for carbohydrate bindingACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2010Svetlana Petkun Family 3 carbohydrate-binding modules (CBM3s) are associated with both cellulosomal scaffoldins and family 9 glycoside hydrolases (GH9s), which are multi-modular enzymes that act on cellulosic substrates. CBM3s bind cellulose. X-ray crystal structures of these modules have established an accepted cellulose-binding mechanism based on stacking interactions between the sugar rings of cellulose and a planar array of aromatic residues located on the CBM3 surface. These planar-strip residues are generally highly conserved, although some CBM3 sequences lack one or more of these residues. In particular, CBM3b, from Clostridium thermocellum Cel9V exhibits such sequence changes and fails to bind cellulosic substrates. A crystallographic investigation of CBM3b, has been initiated in order to understand the structural reason(s) for this inability. CBM3b, crystallized in space group C2221 (diffraction was obtained to 2.0,Å resolution in-house) with three independent molecules in the asymmetric unit and in space group P41212 (diffraction was obtained to 1.79,Å resolution in-house and to 1.30,Å resolution at a synchrotron) with one molecule in the asymmetric unit. The molecular structure of Cel9V CBM3b, revealed that in addition to the loss of several cellulose-binding residues in the planar strip, changes in the backbone create a surface `hump' which could interfere with the formation of cellulose,protein surface interactions and thus prevent binding to crystalline cellulose. [source] The effect of a proline residue on the rate of growth and the space group of ,-spectrin SH3-domain crystalsACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2009Ana Cámara-Artigas ,-Spectrin SH3-domain (Spc-SH3) crystallization is characterized by very fast growth of the crystals in the presence of ammonium sulfate as a precipitant agent. The origin of this behaviour can be attributed to the presence of a proline residue that participates in a crystal contact mimicking the binding of proline-rich sequences to SH3 domains. This residue, Pro20, is located in the RT loop and is the main contact in one of the interfaces present in the orthorhombic Spc-SH3 crystal structures. In order to understand the molecular interactions that are responsible for the very fast crystal growth of the wild-type (WT) Spc-SH3 crystals, the crystal structure of a triple mutant in which the residues Ser19-Pro20-Arg21 in the RT loop have been replaced by Gly19-Asp20-Ser21 (GDS Spc-SH3 mutant) has been solved. The removal of the critical proline residue results in slower nucleation of the Spc-SH3 crystals and a different arrangement of the protein molecules in the unit cell, leading to a crystal that belongs to the tetragonal space group P41212, with unit-cell parameters a = b = 42.231, c = 93.655,Å, and that diffracts to 1.45,Å resolution. For both WT Spc-SH3 and the GDS mutant, light-scattering experiments showed that a dimer was formed in solution within a few minutes of the addition of 2,M ammonium sulfate at pH 6.5 and allowed the proposal of a mechanism for the nucleation and crystal growth of Spc-SH3 in which the Pro20 residue plays a key role in the rate of crystal growth. [source] Crystallization and preliminary X-ray diffraction studies of catalase,peroxidase from Synechococcus PCC 7942ACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2002Kei Wada The recombinant catalase,peroxidase of Synechococcus PCC 7942 overexpressed in Escherichia coli was purified and crystallized by the hanging-drop vapour-diffusion method using sodium formate as a precipitant. The crystals belonged to the tetragonal space group P41212 or P43212, with unit-cell parameters a = b = 109.3, c = 202.0,Å. The calculated VM value based on a dimer in the asymmetric unit was 1.9,Å3,Da,1. A native data set was collected to 2.3,Å resolution from a frozen crystal using synchrotron radiation at SPring-8. [source] Crystallization and preliminary X-ray diffraction analysis of cytotoxic ribonucleases from bullfrog Rana catesbeianaACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2001Jyung-Hurng Liu RC-RNases are ribonucleases from Rana catesbeiana oocytes with pyrimidine,guanine sequence specificity. They also possess cell cytotoxicity and lectin activity. Protein crystals of three RC-RNase isozymes, RC-RNase 3, RC-RNase 4 and RC-RNase 6, were grown in various crystal systems under different conditions. Crystals of RC-RNase3 belong to the orthorhombic C2221 space group, with unit-cell parameters a = 66.66, b = 97.38, c = 85.74,Å. Crystals of RC-RNase 4 belong to the trigonal space group P31 or P32, with unit-cell parameters a = b = 32.22, c = 92.12,Å. Crystals of RC-RNase 6 complexed with cytidylyl 2,-5, guanosine belong to the tetragonal space group P41212 or P43212, with unit-cell parameters a = b = 61.80, c = 65.96,Å. [source] Cloning, expression, purification and preliminary X-ray crystallographic studies of yeast Hsp40 Sis1 complexed with Hsp70 Ssa1 C-terminal lid domainACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2001Xinguo Qian Heat-shock protein 70 (Hsp70) plays essential roles in a number of cellular processes such as protein folding, assembly and translocation. Heat-shock protein 40 (Hsp40) transiently interacts with Hsp70 and facilitates Hsp70 functions in these processes within cells. Hsp40 recognizes and binds non-native polypeptide and delivers it to Hsp70. Hsp40 can then stimulate the ATPase activity of Hsp70 to refold the polypeptide. To investigate the molecular mechanism by which Hsp40 interacts with Hsp70 to transport the non-native polypeptide, Saccharomyces cerevisiae Hsp40 Sis1 C-terminal peptide-binding fragment complexed with Hsp70 Ssa1 C-terminal lid domain has been produced and crystallized. The complex crystals diffract to 3.3,Å and belong to the space group P41212 or P43212, with unit-cell parameters a = 112.17, c = 171.31,Å. Structure determination by the MAD method is under way. [source] Crystallization and preliminary X-ray diffraction analysis of protein l -isoaspartyl O -methyltransferase from wheat germACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2001Michelle D. Amaral Wheat-germ protein l -isoaspartyl O -methyltransferase (WPIMT) can initiate the conversion of l -isoaspartyl residues in a protein or peptide, which accumulate during the aging process in wheat-germ seeds, to normal l -aspartyl groups. The recombinant protein of WPIMT was overexpressed in Escherichia coli and purified to homogeneity. The protein was crystallized in the presence of S -adenosine- l -homocysteine using 2-methyl-2,4-pentanediol. Preliminary X-ray analysis indicated a tetragonal space group P41212 or P43212, with unit-cell parameters a = b = 77.3, c = 152.9,Å for cryofrozen crystals at 90,K. The crystals diffracted to 3.3,Å and contain two molecules per asymmetric unit. [source] Crystallization and preliminary X-ray crystallographic analysis of thioesterase I from Escherichia coliACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2000Yu-Chih Lo The Escherichia coli thioesterase I specifically catalyzes the deacylation of fatty acyl,CoA thioesters, especially those with long acyl groups (C12,C18). Single crystals of thioesterase I (E.C. 3.1.2.2) from E. coli have been obtained using methoxypolyethylene glycol 5000 (PEG,MME 5K) as a precipitant at room temperature in 21,d. The crystals belong to the tetragonal space group P41212 or its enantiomorph P43212, with unit-cell parameters a = b = 50.85,(7), c = 171.5,(1),Å. The crystals diffract to beyond 2.4,Å resolution. There is one molecule of molecular weight 20.5,kDa in the asymmetric unit, with a solvent content of 55%. [source] Crystallization and preliminary X-ray analysis of PaaAC, the main component of the hydroxylase of the Escherichia coli phenylacetyl-coenzyme A oxygenase complexACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2010Andrey M. Grishin The Escherichia coli paa operon encodes enzymes of the phenylacetic acid-utilization pathway that metabolizes phenylacetate in the form of a coenzyme A (CoA) derivative. The phenylacetyl-coenzyme A oxygenase complex, which has been postulated to contain five components designated PaaABCDE, catalyzes ring hydroxylation of phenylacetyl-CoA. The PaaAC subcomplex shows low sequence similarity to other bacterial multicomponent monooxygenases (BMMs) and forms a separate branch on the phylogenetic tree. PaaAC, which catalyzes the hydroxylation reaction, was purified and crystallized in the absence of a bound ligand as well as in complexes with CoA, 3-hydroxybutyryl-CoA, benzoyl-CoA and the true substrate phenylacetyl-CoA. Crystals of the ligand-free enzyme belonged to space group P212121 and diffracted to 2.65,Å resolution, whereas complexes with CoA and its derivatives crystallized in space group P41212 and diffracted to ,2.0,Å resolution. PaaAC represents the first crystallized BMM hydroxylase that utilizes a CoA-linked substrate. [source] Crystallization and preliminary crystallographic analysis of the Magnetospirillum magneticum AMB-1 and M. gryphiswaldense MSR-1 magnetosome-associated proteins MamAACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2010Natalie Zeytuni MamA is a unique magnetosome-associated protein that is predicted to contain six sequential tetratricopeptide-repeat (TPR) motifs. The TPR structural motif serves as a template for protein,protein interactions and mediates the assembly of multi-protein complexes. Here, the crystallization and preliminary X-ray analysis of recombinant and purified Magnetospirillum magneticum and M.,gryphiswaldense MamA are reported for the first time. M. gryphiswaldense MamA,41 crystallized in the tetragonal space group P41212 or P43212, with unit-cell parameters a = b = 58.88, c = 144.09,Å. M. magneticum MamA,41 crystallized in the orthorhombic space group P212121, with unit-cell parameters a = 44.75, b = 76.19, c = 105.05,Å. X-ray diffraction data were collected to resolutions of 2.0 and 1.95,Å, respectively. [source] Purification, crystallization and X-ray crystallographic analysis of Archaeoglobus fulgidus neelaredoxinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2010Tiago M. Bandeiras Neelaredoxins are a type of superoxide reductase (SOR), which are blue 14,kDa metalloproteins with a catalytic nonhaem iron centre coordinated by four histidines and one cysteine in the ferrous form. Anaerobic organisms such as Archaeoglobus fulgidus, a hyperthermophilic sulfate-reducing archaeon, have developed defence mechanisms against toxic oxygen species in which superoxide reductases play a key role. SOR is responsible for scavenging toxic superoxide anion radicals (O2·,), catalysing the one-electron reduction of superoxide to hydrogen peroxide. Crystals of recombinant A. fulgidus neelaredoxin in the oxidized form (13.7,kDa, 125 residues) were obtained using polyethylene glycol and ammonium sulfate. These crystals diffracted to 1.9,Å resolution and belonged to the tetragonal space group P41212, with unit-cell parameters a = b = 75.72, c = 185.44,Å. Cell-content analysis indicated the presence of a tetramer in the asymmetric unit, with a Matthews coefficient (VM) of 2.36,Å3,Da,1 and an estimated solvent content of 48%. The three-dimensional structure was determined by the MAD method and is currently under refinement. [source] Crystallization and preliminary crystallographic studies of the catalytic subunits of human pyruvate dehydrogenase phosphatase isoforms 1 and 2ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2010Junko Kato Pyruvate dehydrogenase phosphatase (PDP) is a mitochondrial serine phosphatase that activates phosphorylated pyruvate dehydrogenase complex by dephosphorylation. In humans, two PDP isoforms (1 and 2) have been identified. PDP1 is composed of a catalytic subunit (PDP1c) and a regulatory subunit (PDP1r), whereas PDP2 consists of only a catalytic subunit (PDP2c). Both PDP1c and PDP2c have been crystallized individually and complete X-ray diffraction data sets have been collected to 2.45 and 2.0,Å resolution, respectively. The PDP1c crystals belonged to space group P41212 or P43212, with unit-cell parameters a = b = 65.1, c = 216.1,Å. The asymmetric unit is expected to contain one molecule, with a Matthews coefficient VM of 2.56,Å3,Da,1. The PDP2c crystals belonged to space group P212121, with unit-cell parameters a = 53.6, b = 69.1, c = 109.7,Å. The asymmetric unit is expected to contain one molecule, with a Matthews coefficient VM of 1.91,Å3,Da,1. [source] Crystallization and preliminary X-ray diffraction analysis of diaminopimelate epimerase from Escherichia coliACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2010Lilian Hor Diaminopimelate (DAP) epimerase (EC 5.1.1.7) catalyzes the penultimate step of lysine biosynthesis in bacteria and plants, converting l,l -diaminopimelate to meso -diaminopimelate. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DAP epimerase from Escherichia coli are presented. Crystals were obtained in space group P41212 and diffracted to 2.0,Å resolution, with unit-cell parameters a = b = 89.4, c = 179.6,Å. Molecular replacement was conducted using Bacillus anthracis DAP epimerase as a search model and showed the presence of two molecules in the asymmetric unit, with an initial Rfree of 0.456 and Rwork of 0.416. [source] Expression, crystallization and preliminary X-ray diffraction analysis of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2009Hyun-Ju Lee Modification (HsdM) and specificity (HsdS) subunits are constituents of an active methyltransferase (MTase) of multifunctional type I restriction enzymes. To provide a molecular background on HsdM, a putative hsdM gene from Vibrio vulnificus YJ016 (HsdM_Vv) was cloned and the expressed protein was purified and crystallized from 22%(w/v) polyethylene glycol 8000, 0.02,M imidazole pH 7.5 and 5,mM,-mercaptoethanol. Diffraction data were collected to 1.86,Å resolution using synchrotron radiation. The crystal belonged to the tetragonal space group P41212 or P43212, with unit-cell parameters a = b = 78.9, c = 165.8,Å. With one molecule in the asymmetric unit, the crystal volume per unit protein weight was 2.12,Å3,Da,1, with a solvent content of 42%. [source] Crystallization and preliminary X-ray diffraction characterization of RpfF, a key DSF synthase from Stenotrophomonas maltophiliaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 10 2009Xian-Ya Lin Stenotrophomonas maltophilia has emerged as a critical nosocomial opportunistic pathogen in the last few years. It is resistant to many clinically useful antibiotics; hence, new ways of combatting this bacterium are essential. Diffusible signal factor (DSF) dependent quorum sensing is a major mechanism of virulence induction in S. maltophilia, with RpfF playing a key role in DSF biosynthesis. Inhibiting S. maltophilia RpfF (SmRpfF) function via small-molecule interference may constitute a new way of treating S. maltophilia infection. SmRpfF was therefore overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to the tetragonal space group P41212 or P43212, with unit-cell parameters a = b = 148.51, c = 122.82,Å, and diffracted to a resolution of 2.25,Å. [source] Crystallization and preliminary X-ray diffraction analysis of the C-terminal domain of the human spliceosomal DExD/H-box protein hPrp22ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2009Denis Kudlinzki The Homo sapiens DExD/H-box protein hPrp22 is a crucial component of the eukaryotic pre-mRNA splicing machinery. Within the splicing cycle, it is involved in the ligation of exons and generation of the lariat and it additionally catalyzes the release of mature mRNA from the spliceosomal U5 snRNP. The yeast homologue of this protein, yPrp22, shows ATP-dependent RNA-helicase activity and is capable of unwinding RNA/RNA duplex molecules. A truncated construct coding for residues 950,1183 of human Prp22, comprising the structurally and functionally uncharacterized C-terminal domain, was cloned into an Escherichia coli expression vector. The protein was subsequently overproduced, purified and crystallized. The crystals obtained diffracted to 2.1,Å resolution, belonged to the tetragonal space group P41212 or P43212, with unit-cell parameters a = b = 78.2, c = 88.4,Å, and contained one molecule in the asymmetric unit. [source] Structure of the twin-arginine signal-binding protein DmsD from Escherichia coliACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Suresh Kumar Ramasamy The translocation of folded proteins via the twin-arginine translocation (Tat) pathway is regulated to prevent the futile export of inactive substrate. DmsD is part of a class of cytoplasmic chaperones that play a role in preventing certain redox proteins from premature transport. DmsD from Escherichia coli has been crystallized in space group P41212, with unit-cell parameters a = b = 97.45, c = 210.04,Å, in the presence of a small peptide. The structure has been solved by molecular replacement to a resolution of 2.4,Å and refined to an R factor of 19.4%. There are four molecules in the asymmetric unit that may mimic a higher order structure in vivo. There appears to be density for the peptide in a predicted binding pocket, which lends support to its role as the signal-recognition surface for this class of proteins. [source] Crystallization and preliminary X-ray analysis of the NADPH-dependent 3-quinuclidinone reductase from Rhodotorula rubraACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2009Daijiro Takeshita (R)-3-Quinuclidinol is a useful compound that is applicable to the synthesis of various pharmaceuticals. The NADPH-dependent carbonyl reductase 3-quinuclidinone reductase from Rhodotorula rubra catalyzes the stereospecific reduction of 3-quinuclidinone to (R)-3-quinuclidinol and is expected to be utilized in industrial production of this alcohol. 3-Quinuclidinone reductase from R. rubra was expressed in Escherichia coli and purified using Ni-affinity and ion-exchange column chromatography. Crystals of the protein were obtained by the sitting-drop vapour-diffusion method using PEG 8000 as the precipitant. The crystals belonged to space group P41212, with unit-cell parameters a = b = 91.3, c = 265.4,Å, and diffracted X-rays to 2.2,Å resolution. The asymmetric unit contained four molecules of the protein and the solvent content was 48.4%. [source] Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the SH3 domain of human AHI1ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2009Zhuliang Shi The SH3 domain of human AHI1 was cloned and expressed in Escherichia coli. The protein was purified by affinity and size-exclusion chromatography and was crystallized using the sitting-drop vapour-diffusion method at 293,K. A complete data set was collected to 2.5,Å resolution at 110,K. The crystal belonged to space group P41212, with unit-cell parameters a = 67.377, b = 67.377, c = 98.549,Å. [source] Overexpression, purification and crystallization of a thermostable DNA ligase from the archaeon Thermococcus sp.ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2009DNA ligases catalyze the sealing of 5,-phosphate and 3,-hydroxyl termini at single-strand breaks in double-stranded DNA and their function is essential to maintain the integrity of the genome in DNA metabolism. An ATP-dependent DNA ligase from the archaeon Thermococcus sp. 1519 was overexpressed, purified and crystallized. Crystals were obtained using the hanging-drop vapour-diffusion method employing 35%(v/v) Tacsimate pH 7.0 as a precipitant and diffracted X-rays to 3.09,Å resolution. They belonged to space group P41212, with unit-cell parameters a = b = 79.7, c = 182.6,Å. [source] Crystallization and preliminary X-ray diffraction analysis of human seminal plasma protein PSP94ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2009Mukesh Kumar The human seminal plasma protein PSP94 is a small protein of 94 residues that contains ten cysteines. Since its discovery about 25,years ago, several potential biological functions have been reported for this protein. Many PSP94 homologues have also been identified since then from various species, but no crystal structure has been determined to date. PSP94 has been purified from human seminal plasma and crystallized. These crystals diffracted to ,2.3,Å resolution and belonged to space group P41212, with unit-cell parameters a = 107.9, b = 107.9, c = 92.1,Å. There are four molecules in the asymmetric unit. Structure solution by the heavy-atom method is currently in progress. [source] Crystallization and preliminary X-ray crystallographic analysis of SMU.412c protein from the caries pathogen Streptococcus mutansACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2009Zhao-Yang Ye The smu.412c gene encodes a putative histidine triad-like protein (SMU.412c) with 139 residues that is involved in cell-cycle regulation in Streptococcus mutans. The gene was cloned into the expression vector pET28a and subsequently expressed in Escherichia coli strain BL21 (DE3) to give a substantially soluble form of SMU.412c with a His6 tag at its N-terminus. The recombinant protein was purified to homogeneity in a two-step procedure involving Ni2+ -chelating and size-exclusion chromatography. Crystals suitable for X-ray diffraction were obtained using the sitting-drop vapour-diffusion method and diffracted to 1.8,Å resolution on beamline BL6A at Photon Factory, Tsukuba, Japan. The crystal belonged to space group P41212, with unit-cell parameters a = b = 53.5, c = 141.1,Å. [source] Crystallization and preliminary characterization of the Thermus thermophilus RNA helicase Hera C-terminal domainACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2009Markus G. Rudolph Heat-resistant RNA-dependent ATPase (Hera) from Thermus thermophilus is a DEAD-box RNA helicase. Two constructs encompassing the second RecA-like domain and the C-terminal domain of Hera were overproduced in Escherichia coli and purified to homogeneity. Single crystals of both Hera constructs were obtained in three crystal forms. A tetragonal crystal form belonged to space group P41212, with unit-cell parameters a = 65.5, c = 153.0,Å, and contained one molecule per asymmetric unit. Two orthorhombic forms belonged to space group P212121, with unit-cell parameters a = 62.8, b = 70.9, c = 102.3,Å (form I) and a = 41.6, b = 67.6, c = 183.5,Å (form II). Both orthorhombic forms contained two molecules per asymmetric unit. All crystals diffracted X-rays to beyond 3,Å resolution, but the tetragonal data sets displayed high Wilson B values and high mean |E2, 1| values, indicating potential disorder and anisotropy. The tetragonal crystal was phased by MAD using a single selenium site. [source] Expression, purification, crystallization and preliminary crystallographic study of the carboxyl-terminal domain of the human voltage-gated proton channel Hv1ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2009Shu Jie Li The voltage-gated proton channel Hv1 is essential to proton permeation and contains a voltage-sensor domain without a pore domain. It contains three predicted domains: an N-terminal acid and proline-rich domain, a transmembrane voltage-sensor domain and a C-terminal domain that is responsible for the dimeric architecture of Hv1. Here, the C-terminal domain of the human voltage-gated proton channel Hv1 (C-Hv1) was overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals have a tetragonal form and diffraction data were collected to 2.5,Å resolution in-house. The crystal belongs to space group P41212, with unit-cell parameters a = b = 37.76, c = 137.52,Å. Structural determination of C-Hv1 is in progress. [source] Crystallization and preliminary X-ray diffraction analysis of a complex between the electron-transfer partners hexameric Cu-containing nitrite reductase and pseudoazurinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2009Daisuke Hira The complex between Cu-containing nitrite reductase (HdNIR) and its electron-donor protein pseudoazurin (HdPAz) from Hyphomicrobium denitrificans has been crystallized. The crystals were obtained from a mixture of the two proteins using the hanging-drop vapour-diffusion method in the presence of polyethylene glycol (PEG) and 2-methyl-2,4-pentanediol (MPD) as precipitants. SDS,PAGE analysis demonstrated that the crystals contained both proteins. The X-ray diffraction experiment was carried out at SPring-8 and diffraction data were collected to 3.3,Å resolution. The crystals were tetragonal (space group P41212), with unit-cell parameters a = b = 130.39, c = 505.55,Å. Preliminary analysis indicated that there was one HdNIR and at least two HdPAz molecules in the asymmetric unit of the crystal. [source] Cloning, expression and purification of cytochrome c6 from the brown alga Hizikia fusiformis and complete X-ray diffraction analysis of the structureACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2008Hideharu Akazaki The primary sequence of cytochrome c6 from the brown alga Hizikia fusiformis has been determined by cDNA cloning and the crystal structure has been solved at 1.6,Å resolution. The crystal belonged to the tetragonal space group P41212, with unit-cell parameters a = b = 84.58, c = 232.91,Å and six molecules per asymmetric unit. The genome code, amino-acid sequence and crystal structure of H. fusiformis cytochrome c6 were most similar to those of red algal cytochrome c6. These results support the hypothesis that brown algae acquired their chloroplasts via secondary endosymbiosis involving a red algal endosymbiont and a eukaryote host. [source] Purification, crystallization and preliminary X-ray analysis of the peptidoglycan N -acetylglucosamine deacetylase BC1960 from Bacillus cereus in the presence of its substrate (GlcNAc)6ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2008Aleka Tsalafouta The peptidoglycan N -acetylglucosamine (GlcNAc) deacetylase BC1960 from Bacillus cereus (EC 3.5.1.33), an enzyme consisting of 275 amino acids, was crystallized in the presence of its substrate (GlcNAc)6. The crystals belonged to the tetragonal space group P41212, with unit-cell parameters a = b = 92.7, c = 242.9,Å and four molecules in the asymmetric unit. A complete data set was collected at 100,K to a resolution of 2.38,Å using synchrotron radiation. [source] Crystallization and preliminary X-ray diffraction analysis of the small laccase from Streptomyces coelicolorACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2007Tereza Skálová The small bacterial laccase from the actinobacterium Streptomyces coelicolor which lacks the second of the three domains of the laccases structurally characterized to date was crystallized. This multi-copper phenol oxidase crystallizes in a primitive tetragonal lattice, with unit-cell parameters a = b = 179.8, c = 175.3,Å. The crystals belong to either space group P41212 or P43212. The self-rotation function shows the presence of a noncrystallographic threefold axis in the structure. Phases will be determined from the anomalous signal of the natively present copper ions. [source] Expression, purification, crystallization and preliminary crystallographic analysis of the proliferation-associated protein Ebp1ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2007Eva Kowalinski ErbB-3-binding protein 1 (Ebp1) is a member of the family of proliferation-associated 2G4 proteins (PA2G4s) and plays a role in cellular growth and differentiation. Ligand-induced activation of the transmembrane receptor ErbB3 leads to dissociation of Ebp1 from the receptor in a phosphorylation-dependent manner. The non-associated protein is involved in transcriptional and translational regulation in the cell. Here, the overexpression, purification, crystallization and preliminary crystallographic studies of Ebp1 from Homo sapiens are reported. Initially observed crystals were improved by serial seeding to single crystals suitable for data collection. The optimized crystals belong to the tetragonal space group P41212 or P43212 and diffracted to a resolution of 1.6,Å. [source] Structure of the T109S mutant of Escherichia coli dihydroorotase complexed with the inhibitor 5-fluoroorotate: catalytic activity is reflected by the crystal formACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2007Mihwa Lee Crystals of a single-point mutant (T109S) of Escherichia coli dihydroorotase (DHOase) with diminished activity grown in the presence of l -dihydroorotate (l -DHO) are tetragonal, with a monomer in the asymmetric unit. These crystals are extremely unstable and disintegrate shortly after formation, which is followed by the growth of orthorhombic crystals from the remnants of the tetragonal crystals or at new nucleation sites. Orthorhombic crystals, for which a structure has previously been reported [Thoden et al. (2001), Biochemistry, 40, 6989,6997; Lee et al. (2005), J. Mol. Biol.348, 523,533], contain a dimer of DHOase in the asymmetric unit; the active site of one monomer contains the substrate N -carbamyl- l -aspartate (l -CA-asp) and the active site of the other monomer contains the product of the reaction, l -DHO. In the subunit with l -DHO in the active site, a surface loop (residues 105,115) is `open'. In the other subunit, with l -CA-asp in the active site, the loop folds inwards, forming specific hydrogen bonds from the loop to the l -CA-asp. The tetragonal crystal form can be stabilized by crystallization in the presence of the inhibitor 5-fluoroorotate (FOA), a product (l -DHO) mimic. Crystals of the complex of T109S DHOase with FOA are tetragonal, space group P41212, with unit-cell parameters a = b = 72.6, c = 176.1,Å. The structure has been refined to R and Rfree values of 0.218 and 0.257, despite severe anisotropy of the diffraction. In this structure, the flexible loops are both in the `open' conformation, which is consistent with FOA, like l -DHO, binding at both sites. The behaviour of the T109S mutant crystals of DHOase in the presence of l -DHO is explained by initial binding of l -DHO to both subunits, followed by slow conversion to l -CA-asp, with consequent movement of the flexible loop and dissolution of the crystals. Orthorhombic crystals are then able to grow in the presence of l -DHO and l -CA-asp. [source] Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription elongation factors GreB from Escherichia coli and Gfh1 from Thermus thermophilusACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2006Anna A. Perederina The Escherichia coli gene encoding the transcription cleavage factor GreB and the Thermus thermophilus gene encoding the anti-GreA transcription factor Gfh1 were cloned and expressed and the purified proteins were crystallized by the sitting-drop vapor-diffusion technique. The GreB and Gfh1 crystals, which were improved by macroseeding, belong to space group P41212 (or P43212), with unit-cell parameters a = b = 148, c = 115.2,Å and a = b = 59.3, c = 218.9,Å, respectively. Complete diffraction data sets were collected for the GreB and Gfh1 crystals to 2.6 and 2.8,Å resolution, respectively. Crystals of the selenomethionine proteins were obtained by microseeding using the native protein crystals and diffract as well as the native ones. The structure determination of these proteins is now in progress. [source] | ||||||||||