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Space Group C2221 (space + group_c2221)
Kinds of Space Group C2221 Selected AbstractsCrystal structures of bovine ,-lactoglobulin in the orthorhombic space group C2221FEBS JOURNAL, Issue 2 2001Structural differences between genetic variants A, features of the Tanford transition The crystal structures of ,-lactoglobulin genetic variants A and B have been determined in the orthorhombic space group C2221 (lattice Y) by X-ray diffraction at 2.0 Å and 1.95 Å resolution, respectively. The structural comparison shows that both variants exhibit the open conformation of the EF loop at the pH of crystallization (pH 7.9), in contrast to what has been reported for the same genetic variants at pH 7.1 in the trigonal space group P3221 (lattice Z) [Qin, B.Y., Bewley, M.C., Creamer, L.K., Baker, E.N. & Jameson, G.B. (1999) Protein Sci.8, 75,83]. Furthermore, it was found that the stereochemical environment of Tyr42 changes significantly with pH variation between pH 7 and pH 8. This may provide a structural explanation for an as yet unexplained feature of the Tanford transition, namely the increase in exposure of a tyrosine residue. [source] Structure 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] Structures of aminoglycoside acetyltransferase AAC(6,)-Ii in a novel crystal form: structural and normal-mode analysesACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2005David L. Burk The aminoglycoside-modifying enzyme aminoglycoside 6,- N -acetyltransferase type Ii [AAC(6,)-Ii] has been crystallized with its cofactor coenzyme A in space group C2221, with unit-cell parameters a = 71.5, b = 127.4, c = 76.9,Å and one physiologically relevant dimer species per asymmetric unit. The space group previously observed for this complex was P212121, with two dimers per asymmetric unit. By comparing the six available protomer structures of the AAC(6,)-Ii,CoA complex, it has been possible to identify regions of plasticity within the protein. Normal-mode analysis of this complex suggests that this plasticity is not an artefact of crystal-packing forces, but that the region of the protomer that displays multiple conformations is intrinsically flexible. It is conjectured that the flexibility is relevant for the cooperative activity observed for the enzyme. [source] Crystallization and preliminary X-ray diffraction study of mammalian mitochondrial seryl-tRNA synthetaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2004Sarin Chimnaronk The mitochondrial seryl-tRNA synthetase (mt SerRS) from Bos taurus was overexpressed in Escherichia coli and crystallized using the sitting-drop vapour-diffusion method. Crystals grew in a very narrow range of conditions using PEG 8000 as precipitant at room temperature. An appropriate concentration of lithium sulfate was critical for crystal nucleation. Crystals diffracted well beyond a resolution of 1.6,Å and were found to belong to the orthorhombic space group C2221, with unit-cell parameters a = 79.89, b = 230.42, c = 135.60,Å. There is one dimer (Mr, 113,kDa) in the asymmetric unit, with a solvent content of 55%. Efforts to solve the phase problem by molecular replacement are under way. [source] Expression, purification, crystallization and preliminary crystallographic analysis of phosphoserine aminotransferase from Bacillus alcalophilusACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2003Anatoly P. Dubnovitsky Phosphoserine aminotransferase (PSAT; EC 2.6.1.52) from Bacillus alcalophilus, an obligatory alkalophile with optimum growth at pH 10.6, was overexpressed in Escherichia coli, purified and crystallized under two different conditions using the hanging-drop vapour-diffusion method. Crystals were obtained using trisodium citrate dihydrate or PEG 400 as a precipitating agent. Crystals grown in the presence of trisodium citrate belong to the orthorhombic space group C2221, with unit-cell parameters a = 105.6, b = 136.6, c = 152.0,Å, and those grown in the presence of PEG 400 belong to the orthorhombic space group P21212, with unit-cell parameters a = 143.7, b = 84.3, c = 67.4,Å. Complete data sets were collected to 1.7 and 1.6,Å resolution, respectively, at 100,K using synchrotron radiation. Analysis of the structure of B. alcalophilus PSAT may reveal structural features that contribute to enzyme adaptability at high pH values. [source] An orthorhombic form of Escherichia coli aminopeptidase P at 2.4,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2003Stephen C. Graham Aminopeptidase P (AMPP) from Escherichia coli cleaves the N-terminal residue from an oligopeptide if the second residue is proline. The active site contains a dinuclear metal centre. Following earlier structural analyses of crystals in space groups P6422 and I4122, the structure of AMPP has been solved and refined in the orthorhombic space group C2221 at 2.4,Å resolution. There are six subunits in the asymmetric unit. These are arranged in two types of tetramer. One tetramer comprises four crystallographically independent subunits, while the other comprises two pairs of subunits related by a crystallographic twofold axis. The final model of 20,994 protein atoms, 1618 water molecules and 12 metal atoms refined to residuals R = 0.195 and Rfree = 0.215. The molecular structure confirms most of the previously reported features, including the subunit,subunit interfaces in the tetramer and persistent disorder at some residues. The metal,ligand bond lengths at the active site suggest that one of the two Mn atoms is five-coordinate rather than six-coordinate. [source] Cloning, overexpression, purification, crystallization and preliminary diffraction analysis of the receiver domain of MicAACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2003Colin J. Bent MicA is a response regulator from Streptococcus pneumoniae thought to be involved in redox-energy sensing under oxygen-limiting environments. The purified protein was crystallized using the sitting-drop vapour-diffusion technique. X-ray diffraction data were collected using synchrotron radiation to a resolution of 1.91,Å. The crystals belong to the monoclinic space group C2221, with unit-cell parameters a = 78.69, b = 92.57, c = 37.16,Å, , = , = , = 90.0°. The Matthews coefficient indicates that MicA crystallizes with one molecule in the asymmetric unit. [source] Concanavalin A in a dimeric crystal form: revisiting structural accuracy and molecular flexibilityACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2002Katherine A. Kantardjieff A structure of native concanavalin A (ConA), a hardy perennial of structural biology, has been determined in a dimeric crystal form at a resolution of 1.56,Å (space group C2221; unit-cell parameters a = 118.70, b = 101.38, c = 111.97,Å; two molecules in the asymmetric unit). The structure has been refined to an Rfree of 0.206 (R = 0.178) after iterative model building and phase-bias removal using Shake&wARP. Correspondence between calculated water,tyrosine interactions and experimentally observed structures near the saccharide-binding site suggests that the observed interactions between Tyr12 and water in various crystal forms are to be expected and are not unique to the presence of an active site. The present structure differs from previously reported atomic resolution structures of ConA in several regions and extends insight into the conformational flexibility of this molecule. Furthermore, this third, low-temperature, structure of ConA in a different crystal form, independently refined using powerful model-bias removal techniques, affords the opportunity to revisit assessment of accuracy and precision in high- or atomic resolution protein structures. It is illustrated that several precise structures of the same molecule can differ substantially in local detail and users of crystallographic models are reminded to consider the potential impact when interpreting structures. Suggestions on how to effectively represent ensembles of crystallographic models of a given molecule are provided. [source] Crystallization and preliminary crystallographic analysis of the recombinant N-terminal domain of riboflavin synthaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2001Winfried Meining Riboflavin synthase catalyzes the final step in the biosynthesis of riboflavin. Animals and humans lack this enzyme, whereas many bacteria and certain yeasts are absolutely dependent on endogenous riboflavin synthesis. Riboflavin synthase is therefore an attractive target for chemotherapy. The N-terminal domain of riboflavin synthase forms a dimer in solution and is capable of strongly binding riboflavin. It can serve as a model for the binding site of the native enzyme. Structural information obtained from this domain at high resolution will be helpful in the determination of the binding mode of riboflavin and thus for the development of antimicrobial drugs. Here, the crystallization and preliminary crystallographic analysis of the N-terminal domain of riboflavin synthase are reported. The crystals belong to the space group C2221, with unit-cell parameters a = 50.3, b = 104.7, c = 85.3,Å, , = , = , = 90°, and diffract to 2.6,Å resolution. [source] Crystallization and preliminary X-ray diffraction studies of a novel alkaline serine protease (KP-43) from alkaliphilic Bacillus sp. strain KSM-KP43ACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2001Tsuyoshi Nonaka A novel alkaline serine protease (KP-43) which belongs to a new class of the subtilisin superfamily was crystallized by the sitting-drop vapour-diffusion method with ammonium sulfate as a precipitant. The crystals belong to the orthorhombic space group C2221, with unit-cell parameters a = 43.50,(2), b = 110.4,(1), c = 168.9,(1),Å. The crystals diffract X-rays beyond 1.9,Å resolution using Cu,K, radiation from a rotating-anode generator and are suitable for high-resolution crystal structure analysis. [source] Crystallization and X-ray diffraction studies of the fatty-acid responsive transcription factor FadR from Escherichia coliACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2000Daan M. F. Van Aalten FadR, an acylCoA-dependent Escherichia coli transcription factor controlling the expression of genes involved in fatty-acid degradation and synthesis, has been crystallized. Crystals of two binary complexes were obtained. The FadR,CoA complex crystallized in space group C2221, with unit-cell parameters a = 61.3, b = 102.0, c = 91.3,Å. The FadR,octanoyl-CoA complex crystallized in space group P6522, with unit-cell parameters a = b = 59.7, c = 296.2,Å. Both crystal forms diffracted to 3.5,Å on a rotating-anode generator. In both crystal forms, the asymmetric unit contains one subunit. The protein is known to be a homodimer; each subunit consists of two domains of unknown fold. For the acyl-CoA-binding domain, a previously undetected sequence homology to PAS domains, in particular the photoactive yellow protein, is reported. [source] Overexpression, crystallization and preliminary X-ray crystallographic analysis of Pseudomonas aeruginosa MnmE, a GTPase involved in tRNA modificationACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2010Hyung Ho Lee MnmE, an evolutionarily conserved GTPase, is involved in modification of the uridine base (U34) at the wobble position of certain tRNAs. Previous crystal structures of MnmE suggest that it is a dimer with considerable conformational flexibility. To facilitate structural comparisons among MnmE proteins, structural analysis of MnmE from Pseudomonas aeruginosa encoded by the PA5567 gene was initiated. It was overexpressed in Escherichia coli and crystallized at 297,K using a reservoir solution consisting of 100,mM sodium ADA pH 6.5, 12%(w/v) polyethylene glycol 4000, 100,mM lithium sulfate, 2%(v/v) 2-propanol and 2.5,mM dithiothreitol. X-ray diffraction data were collected to 2.69,Å resolution. The crystals belonged to the orthorhombic space group C2221, with unit-cell parameters a = 96.74, b = 204.66, c = 120.90,Å. Two monomers were present in the asymmetric unit, resulting in a crystal volume per protein mass (VM) of 2.99,Å3,Da,1 and a solvent content of 58.8%. [source] Purification, crystallization and preliminary X-ray analysis of human GIMAP2ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2010David Schwefel GTPases of immunity-associated proteins (GIMAPs) are important regulators of T-cell death and survival. Here, the crystallization and data collection of three GIMAP2 constructs in various nucleotide-loaded states is described. Selenomethionine-substituted carboxy-terminally truncated GIMAP2 (amino-acid residues 1,260; GIMAP21,260) in the nucleotide-free form crystallized in space group P212121 and the crystals diffracted X-rays to 1.5,Å resolution. The phase problem was solved using the single anomalous dispersion (SAD) protocol. GDP-bound GIMAP221,260 and GDP-bound GIMAP21,234 crystallized in space group P212121 and the crystals diffracted X-rays to 2.9 and 1.7,Å resolution, respectively. GTP-bound GIMAP21,234 crystallized in space group C2221 and the crystals diffracted to 1.9,Å resolution. These results will allow a detailed structural analysis of GIMAP2, which will provide insight into the architecture and function of the GIMAP family. [source] Preliminary X-ray crystallographic analysis of SMU.2055 protein from the caries pathogen Streptococcus mutansACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Wang-Hong Zhao The SMU.2055 gene from the major caries pathogen Streptococcus mutans is annotated as a putative acetyltransferase with 163 amino-acid residues. In order to identify its function via structural studies, the SMU.2055 gene was cloned into the expression vector pET28a. Native and SeMet-labelled SMU.2055 proteins with a His6 tag at the N-terminus were expressed at a high level in Escherichia coli strain BL21 (DE3) and purified to homogeneity by Ni2+ -chelating affinity chromatography. Diffraction-quality crystals of SeMet-labelled SMU.2055 were obtained using the sitting-drop vapour-diffusion method and diffracted to a resolution of 2.5,Å on beamline BL17A at the Photon Factory, Tsukuba, Japan. The crystals belong to the orthorhombic space group C2221, with unit-cell parameters a = 92.0, b = 95.0, c = 192.2,Å. The asymmetric unit contained four molecules, with a solvent content of 57.1%. [source] A new crystal form of human diamine oxidaseACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2010Aaron P. McGrath Copper amine oxidases (CAOs) are ubiquitous in nature and catalyse the oxidative deamination of primary amines to the corresponding aldehydes. Humans have three viable CAO genes (AOC1,3). AOC1 encodes human diamine oxidase (hDAO), which is the frontline enzyme for histamine metabolism. hDAO is unique among CAOs in that it has a distinct substrate preference for diamines. The structure of hDAO in space group P212121 with two molecules in the asymmetric unit has recently been reported. Here, the structure of hDAO refined to 2.1,Å resolution in space group C2221 with one molecule in the asymmetric unit is reported. [source] Crystallization and preliminary X-ray analysis of the LOV domain of the blue-light receptor YtvA from Bacillus amyloliquefaciens FZB42ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Hideaki Ogata Light,oxygen,voltage (LOV) proteins play an important role in blue-light-dependent physiological processes in many organisms. The LOV domain of the blue-light receptor YtvA from Bacillus amyloliquefaciens FZB42 has been purified and crystallized at 277,K using the sitting-drop vapour-diffusion method with 2-ethoxyethanol as a precipitant. A data set was collected to 1.60,Å resolution from a single crystal at 100,K using synchrotron radiation. The LOV domain of YtvA crystallized in space group C2221, with unit-cell parameters a = 64.95, b = 83.76, c = 55.81,Å. The crystal structure of the LOV domain of YtvA was determined by the molecular-replacement method. The crystal contained one molecule per asymmetric unit, with a Matthews coefficient (VM) of 3.04,Å3,Da,1; the solvent content was estimated to be 59.5%. [source] Purification, crystallization and preliminary crystallographic studies of a Kunitz-type proteinase inhibitor from tamarind (Tamarindus indica) seedsACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2009Dipak N. Patil A Kunitz-type proteinase inhibitor has been purified from tamarind (Tamarindus indica) seeds. SDS,PAGE analysis of a purified sample showed a homogeneous band corresponding to a molecular weight of 21,kDa. The protein was identified as a Kunitz-type proteinase inhibitor based on N-terminal amino-acid sequence analysis. It was crystallized by the vapour-diffusion method using PEG 6000. The crystals belonged to the orthorhombic space group C2221, with unit-cell parameters a = 37.2, b = 77.1, c = 129.1,Å. Diffraction data were collected to a resolution of 2.7,Å. Preliminary crystallographic analysis indicated the presence of one proteinase inhibitor molecule in the asymmetric unit, with a solvent content of 44%. [source] Crystallization and preliminary crystallographic studies of the recombinant dihydropyrimidinase from Sinorhizobium meliloti CECT4114ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2006Sergio Martínez-Rodríguez Dihydropyrimidinases are involved in the reductive pathway of pyrimidine degradation, catalysing the hydrolysis of 5,6-dihydrouracil and 5,6-dihydrothymine to the corresponding N -carbamoyl ,-amino acids. This enzyme has often been referred to as hydantoinase owing to its industrial application in the production of optically pure amino acids starting from racemic mixtures of 5-monosubstituted hydantoins. Recombinant dihydropyrimidinase from Sinorhizobium meliloti CECT4114 (SmelDhp) has been expressed, purified and crystallized. Crystallization was performed using the counter-diffusion method with capillaries of 0.3,mm inner diameter. Crystals of SmelDhp suitable for data collection and structure determination were grown in the presence of agarose at 0.1%(w/v) in order to ensure mass transport controlled by diffusion. X-ray data were collected to a resolution of 1.85,Å. The crystal belongs to the orthorhombic space group C2221, with unit-cell parameters a = 124.89, b = 126.28, c = 196.10,Å and two molecules in the asymmetric unit. A molecular-replacement solution has been determined and refinement is in progress. [source] Crystallization and preliminary X-ray diffraction study of a cell-wall invertase from Arabidopsis thalianaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2005Maureen Verhaest Cell-wall invertase 1 (AtcwINV1), a plant protein from Arabidopsis thaliana which is involved in the breakdown of sucrose, has been crystallized in two different crystal forms. Crystal form I grows in space group P31 or P32, whereas crystal form II grows in space group C2221. Data sets were collected for crystal forms I and II to resolution limits of 2.40 and 2.15,Å, respectively. [source] Inclusion Behavior of ,-Cyclodextrin with Bipyridine Molecules: Factors Governing Host-Guest Inclusion GeometriesCHEMISTRY - AN ASIAN JOURNAL, Issue 3 2009Yan-Li Zhao Dr. Abstract Guest Effect: The differences of nitrogen atom positions and the bridge bonds linked to two pyridine rings of some bipyridine guests can significantly affect the binding abilities and inclusion geometries of ,-cyclodextrin with the guests in both the solution and solid states. The 1:1 complexation of ,-cyclodextrin (,-CD) with structurally similar bipyridine guests which lead to the formation of six inclusion complexes (1,6) of ,-CD with 4,4,-vinylenedipyridine, 2,2,-vinylenedipyridine, 1-(2-pyridyl)-2-(4-pyridyl)ethylene, 4,4,-ethylene-dipyridine, 4,4,-dithiodipyridine, and 2,2,-dithiodipyridine has been investigated comprehensively by X-ray crystallography in the solid state and by 1H,NMR spectroscopy and microcalorimetric titration in aqueous solution. The complex formation constants (KS) for the stoichiometric 1:1 host,guest inclusion complexation of ,-CD with the bipyridine derivatives were determined in aqueous solution by microcalorimetry and the host,guest inclusion geometries of the complexes were deduced from 1H ROESY NMR spectroscopy. It transpires that the guest bipyridine molecules are included in the ,-CD cavity with a range of different inclusion geometries. In the solid state, the crystal superstructures for the ,-CD complexes 1, 4, and 5 are characterized by the triclinic crystal system (space group P1) commensurate with AAAA type supramolecular aggregation. By contrast, the ,-CD complexes 2, 3, and 6 display either monoclinic (space group P21) or orthorhombic (space group C2221) crystal systems, characteristic of ABAB type supramolecular aggregation. The results demonstrate that the relative locations of the nitrogen atom positions and the bridge-bond links between the two pyridine rings in these bipyridine guests, not only lead to distinct crystal systems and space groups, but also to different binding geometries and thermodynamical parameters on complexation of the bipyridines with ,-CD. The knowledge obtained from this research improves our understanding of the molecular recognition and self-assembly processes exhibited by ,-CD, both in the solid state and in aqueous solution. [source] | ||||||||||