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Native Data (native + data)

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Chemistry95%

Terms modified by Native Data

  • native data set
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    Selected Abstracts

    After BitTorrent: Darknets to Native Data

    ARCHITECTURAL DESIGN, Issue 5 2006
    Anthony Burke
    Abstract What are the implications of the inherent reflexivity of the Internet for the design professions? Anthony Burke argues that radically innovative and distributed forms of information exchange such as BitTorrent suggest a general shift away from the traditional conception of the architect as master builder to one more in line with the collaborative remixing and patching tactics of the hacker. BitTorrent is a communications protocol that allows massive information exchange across infinite users with minimum resources. Through its sheer force of collectively pooled imagination, it provides a potent example of the sorts of platforms of information exchange that foster the new forms of communal organisation that Michael Hardt and Antonio Negri term the ,Multitude', and which productively challenge conventional models of cultural invention and production. In this context, Burke raises questions about the implications of this broader shift for the design professions' business organisation, as well as their more general methodologies. Copyright © 2006 John Wiley & Sons, Ltd. [source]

    Expression, crystallization and preliminary structural analysis of the ectoplasmic region of apical membrane antigen 1 from Plasmodium vivax, a malaria-vaccine candidate

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2004
    Brigitte Vulliez-Le Normand
    Apical membrane antigen 1 (AMA1), a type 1 transmembrane protein present in the microneme organelles of Plasmodium, is a leading malaria-vaccine candidate. The ectoplasmic region of AMA1 from P. vivax has been expressed in Pichia pastoris and crystallized in two different forms: an orthorhombic form (space group P212121, unit-cell parameters a = 54.1, b = 76.1, c = 103.9,Å) and a monoclinic form (space group C2, unit-cell parameters a = 150.0, b = 53.8, c = 60.3,Å, , = 113.2°). Native data have been collected to 2.0,Å resolution for the orthorhombic form and 1.8,Å for the monoclinic form. A platinum derivative was prepared for the orthorhombic and monoclinic crystals using K2PtCl4 and data were collected at several wavelengths to obtain phases by the MAD technique. A partial model has been built from the electron-density maps of both forms and refinement is in progress. [source]

    Crystallization and phasing of focal adhesion protein 52 from Gallus gallus

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2004
    Imre Tör
    Focal adhesion protein 52 (FAP52) is a multidomain adaptor protein of 448 amino acids characterized as an abundant component of focal adhesions. FAP52 binds to filamin via its N-terminal ,-helical domain, suggesting a role in linking focal adhesions to the actin-based cytoskeleton. The recombinant protein was crystallized using the hanging-drop vapour-diffusion method, which yielded two crystal forms. Native data were collected from both crystal forms to 2.8 and 2.1,Å resolution, respectively. For one of the crystal forms, initial MAD phasing was successfully performed using two data sets from xenon-derivatized crystals. The derivative data sets were collected using softer X-rays of 1.5 and 1.9,Å wavelength. Preliminary structural analysis reveals the presence of a dimer in the asymmetric unit. [source]

    Cloning, purification, crystallization and preliminary crystallographic studies of Bradyrhizobium fucosyltransferase NodZ

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2004
    Krzysztof Brzezinski
    The ,-1,6-fucosyltransferase NodZ from Bradyrhizobium sp. WM9 (Lupinus), composed of 325 amino acids with a molecular weight of 37,kDa, has been cloned, expressed and purified. Protein crystals suitable for X-ray diffraction were obtained under optimized crystallization conditions using ammonium dihydrogen phosphate as a precipitant. The crystals are hexagonal and belong to space group P6122 or P6522, with unit-cell parameters a = 125.5, c = 95.6,Å, and contain 56.8% solvent and a single protein molecule in the asymmetric unit. Native data were collected to 2.85,Å using synchrotron radiation and cryogenic conditions. The native crystals were soaked in a mother-liquor solution containing 2.5,mM [Ta6Br12]2+ cluster for derivatization and SAD data were collected to 3.4,Å at the tantalum LIII absorption peak. [source]

    Crystallization and preliminary X-ray analysis of the selenate reductase from Thauera selenatis

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2002
    Megan J. Maher
    Selenate reductase from Thauera selenatis was crystallized using ammonium sulfate as a precipitant. Crystals of selenate reductase belong to the space group C2, with unit-cell parameters a = 116.9, b = 67.5, c = 186.7,Å, , = 90°. Native data to 2.1,Å resolution have been collected and a heavy-atom derivative has been identified following soaking of the crystals in a solution of trimethyl lead acetate. [source]

    High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5,AMP

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2001
    Pascal Retailleau
    Native data, anomalous data at three wavelengths and an independent peak-wavelength data set for SeMet-substituted protein have been collected from cryoprotected crystals of the TrpRS,adenylate product (TAM) complex to a resolution limit of 1.7,Å. Independent phase sets were developed using SHARP and improved by solvent flipping with SOLOMON using molecular envelopes derived from experimental ­densities for, respectively, peak-wavelength SAD data from four different crystals, MAD data and their M(S)IRAS ­combinations with native data. Hendrickson,Lattman phase-probability coefficients from each phase set were used in BUSTER to drive maximum-likelihood refinements of well defined parts of the previously refined room-temperature 2.9,Å structure. Maximum-entropy completion followed by manual rebuilding was then used to generate a model for the missing segments, bound ligand and solvent molecules. Surprisingly, peak-wavelength SAD experiments produced the smallest phase errors relative to the refined structures. Selenomethionylated models deviate from one another by 0.25,Å and from the native model by 0.38,Å, but all have r.m.s. deviations of ,1.0,Å from the 2.9,Å model. Difference Fourier calculations between amplitudes from the 300,K experiment and the new amplitudes at 100,K using 1.7,Å model phases show no significant structural changes arising from temperature variation or addition of cryoprotectant. The main differences between low- and high-resolution structures arise from correcting side-chain rotamers in the core of the protein as well as on the surface. These changes improve various structure-validation criteria. [source]

    Crystallization and preliminary X-ray analysis of RecG, a replication-fork reversal helicase from Thermotoga maritima complexed with a three-way DNA junction

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2001
    Martin R. Singleton
    The monomeric 3,-5, helicase RecG from the thermophilic bacterium Thermotoga maritima has been crystallized in complex with a three-way DNA junction, the preferred physiological substrate. The crystals were obtained by hanging-drop vapour diffusion. The crystals belong to space group C2, with unit-cell parameters a = 133.7, b = 144.6, c = 84.0,Å, , = 113.8°. Native data to a resolution of 3.25,Å were collected from crystals flash-cooled to 100,K. [source]

    Preliminary crystallographic study of Thermus aquaticus glycerol kinase

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2001
    Hua-Shan Huang
    Glycerol kinase (GlpK) is an important enzyme which catalyzes the rate-limiting step in a central biochemical pathway involving glycerol metabolism. GlpK from the thermophile Thermus aquaticus has been overexpressed in glpK -deficient Escherichia coli and crystallized by the hanging-drop method. The crystal belongs to the cubic space group I23, with unit-cell parameters a = b = c = 163.94,(3),Å. Native data were collected to 2.87,Å resolution on a Cu,K, rotating-anode X-ray source. [source]

    Crystallization and preliminary crystallographic studies of an antimicrobial protein from Pharbitis,nil

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2001
    Sung Chul Ha
    An antimicrobial protein from seeds of Pharbitis nil (Pn-AMP) which shows an antifungal activity towards several agriculturally important plant pathogens has been crystallized in the presence of equimolar N -­acetylglucosamine with sodium citrate as precipitant. The crystal belongs to the hexagonal space group P6122 (or P6522), with unit-cell parameters a = b = 29.33,(5), c = 133.44,(12),Å. Native data were collected using a crystal at 100,K to a resolution of 1.78,Å. [source]

    Crystallization and preliminary X-ray analysis of Borrelia burgdorferi outer surface protein C (OspC)

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2001
    D. Kumaran
    Single crystals of the outer surface protein C (OspC) from Borrelia burgdorferi HB19 have been obtained by the vapor-diffusion method. These crystals belong to space group P21, with unit-cell parameters a = 66.218, b = 46.113, c = 112.079,Å, , = 99.30°, and diffract to at least 2.2,Å resolution. Native data have been collected from flash-frozen crystals at the National Synchrotron facility of Brookhaven National Laboratory. There are two dimers per asymmetric unit, related by a non-crystallographic twofold axis and a pseudo-translational symmetry. [source]

    Crystallization and preliminary X-ray analysis of Clostridium botulinum neurotoxin type B

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2000
    S. Swaminathan
    Single crystals of Clostridium botulinum neurotoxin type B have been obtained by the vapor-diffusion method. These crystals belong to space group P21, with unit-cell parameters a = 76.08, b = 123.11, c = 95.86,Å, , = 113.03° and diffract to at least 1.8,Å resolution. Native data have been collected from flash-frozen crystals at the National Synchrotron facility of Brookhaven National Laboratory. These crystals often tend to be non-isomorphic. [source]

    Crystallization and preliminary crystallographic analysis of nosiheptide-resistance methyltransferase from Streptomyces actuosus in complex with SAM

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010
    Huirong Yang
    Nosiheptide-resistance methyltransferase (NSR) methylates 23S rRNA at the nucleotide adenosine 1067 in Escherichia coli and thus contributes to resistance against nosiheptide, a sulfur-containing peptide antibiotic. Here, the expression, purification and crystallization of NSR from Streptomyces actuosus are reported. Diffracting crystals were grown by the hanging-drop vapour-diffusion method in reservoir solution consisting of 0.35,M ammonium chloride, 24%(w/v) PEG 3350, 0.1,M MES pH 5.7 at 293,K. Native data have been collected from the apo enzyme and a SAM complex, as well as apo SeMet SAD data. The diffraction patterns of the apo form of NSR, of NSR complexed with SAM and of SeMet-labelled NSR crystals extended to 1.90, 1.95 and 2.25,Å resolution, respectively, using synchrotron radiation. All crystals belonged to space group P21, with approximate unit-cell parameters a = 64.6, b = 69.6, c = 64.9,Å, , = 117.8°. [source]

    Purification, crystallization and preliminary X-ray analysis of the HsdR subunit of the EcoR124I endonuclease from Escherichia coli

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2007
    Mikalai Lapkouski
    EcoR124I is a multicomplex enzyme belonging to the type I restriction-modification system from Escherichia coli. Although EcoR124I has been extensively characterized biochemically, there is no direct structural information available about particular subunits. HsdR is a motor subunit that is responsible for ATP hydrolysis, DNA translocation and cleavage of the DNA substrate recognized by the complex. Recombinant HsdR subunit was crystallized using the sitting-drop vapour-diffusion method. Crystals belong to the primitive monoclinic space group, with unit-cell parameters a = 85.75, b = 124.71, c = 128.37,Å, , = 108.14°. Native data were collected to 2.6,Å resolution at the X12 beamline of EMBL Hamburg. [source]

    Crystallization and preliminary X-ray analysis of the aromatic prenyltransferase CloQ from the clorobiocin biosynthetic cluster of Streptomyces roseochromogenes

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2006
    Sascha Keller
    Crystals of recombinant CloQ (subunit MW = 35,626,Da; 324 amino acids), an aromatic prenyltransferase from Streptomyces roseochromogenes, were grown by vapour diffusion. The protein crystallizes in space group I4122, with unit-cell parameters a = b = 135.19, c = 98.13,Å. Native data from a single crystal were recorded to a resolution of 2.2,Å in-house. Preliminary analysis of these data indicated that the asymmetric unit corresponds to a monomer, giving an estimated solvent content of 60.6%. CloQ is involved in the biosynthesis of the aminocoumarin antibiotic clorobiocin, which targets the essential bacterial enzyme DNA gyrase. [source]

    Expression, purification, crystallization and preliminary X-ray analysis of two arginine-biosynthetic enzymes from Mycobacterium tuberculosis

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 10 2006
    Fatemeh Moradian
    The gene products of two open reading frames from Mycobacterium tuberculosis (Mtb) have been crystallized using the sitting-drop vapour-diffusion method. Rv1652 encodes a putative N -acetyl-,-glutamyl-phosphate reductase (MtbAGPR), while the Rv1656 gene product is annotated as ornithine carbamoyltransferase (MtbOTC). Both MtbAGPR and MtbOTC were expressed in Escherichia coli, purified to homogeneity and crystallized. Native data for each crystal were collected to resolutions of 2.15 and 2.80,Å, respectively. Preliminary X-ray data are presented for both enzymes. [source]

    Iodide-SAD, SIR and SIRAS phasing for structure solution of a nucleosome assembly protein

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009
    Manickam Yogavel
    The crystal structure of Plasmodium falciparum nucleosome assembly protein (PfNapL) was determined by iodide-SAD/SIRAS phasing methods using iodide-SAD data to 3.0,Å resolution and native data to 2.4,Å resolution. Halide-derivatized PfNapL crystals were obtained using the quick cryo-soaking method in which the native crystals were soaked in a cryosolution consisting of 500,mM NaI for a short period of 30,60,s and data were collected at an in-house X-ray source using Cu,K, radiation. Despite a low anomalous signal-to-noise ratio of <1.2 in the >3.5,Å resolution bin, the data were sufficient to determine the structure by SAD/SIR/SIRAS methods using the soaked iodides. Previously, structure solution had failed with both molecular-replacement and selenomethionine-derivatization techniques owing to reasons that are detailed in this work. The phasing at low resolution with three iodides per monomer with high temperature factors was successful using any of the SAD, SIR or SIRAS methods. [source]

    Structure of xylanase Xys1, from Streptomyces halstedii

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2003
    Albert Canals
    Xylanases hydrolyze the ,-1,4-linked xylose backbone of xylans. They are of increasing interest in the paper and food industries for their pre-bleaching and bio-pulping applications. Such industries demand new xylanases to cover a wider range of cleavage specificity, activity and stability. The catalytic domain of xylanase Xys1 from Streptomyces halstedii JM8 was expressed, purified and crystallized and native data were collected to 1.78,Å resolution with an Rmerge of 4.4%. The crystals belong to space group P212121, with unit-cell parameters a = 34.05, b = 79.60, c = 87.80,Å. The structure was solved by the molecular-replacement method using the structure of the homologue Xyl10A from Streptomyces lividans. In a similar manner to other members of its family, Xys1 folds to form a standard (,/,)8 barrel with the two catalytic functions, the acid/base and the nucleophile, at its C-­terminal side. The overall structure is described and compared with those of related xylanases. [source]

    High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5,AMP

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2001
    Pascal Retailleau
    Native data, anomalous data at three wavelengths and an independent peak-wavelength data set for SeMet-substituted protein have been collected from cryoprotected crystals of the TrpRS,adenylate product (TAM) complex to a resolution limit of 1.7,Å. Independent phase sets were developed using SHARP and improved by solvent flipping with SOLOMON using molecular envelopes derived from experimental ­densities for, respectively, peak-wavelength SAD data from four different crystals, MAD data and their M(S)IRAS ­combinations with native data. Hendrickson,Lattman phase-probability coefficients from each phase set were used in BUSTER to drive maximum-likelihood refinements of well defined parts of the previously refined room-temperature 2.9,Å structure. Maximum-entropy completion followed by manual rebuilding was then used to generate a model for the missing segments, bound ligand and solvent molecules. Surprisingly, peak-wavelength SAD experiments produced the smallest phase errors relative to the refined structures. Selenomethionylated models deviate from one another by 0.25,Å and from the native model by 0.38,Å, but all have r.m.s. deviations of ,1.0,Å from the 2.9,Å model. Difference Fourier calculations between amplitudes from the 300,K experiment and the new amplitudes at 100,K using 1.7,Å model phases show no significant structural changes arising from temperature variation or addition of cryoprotectant. The main differences between low- and high-resolution structures arise from correcting side-chain rotamers in the core of the protein as well as on the surface. These changes improve various structure-validation criteria. [source]

    Structure of lobster apocrustacyanin A1 using softer X-rays

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2001
    M. 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 X-ray crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Saccharomyces cerevisiae

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2001
    Byung Woo Han
    Deoxyuridine triphosphate nucleotidohydrolase (dUTPase) from Saccharomyces cerevisiae is essential for cell viability. It has been overexpressed in Escherichia coli and has been crystallized at 296,K using polyethylene glycol (PEG) 1500 as a precipitant. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 59.48, b = 138.54, c = 157.91,Å, , = , = , = 90°. Two molecules of trimeric dUTPase from S. cerevisiae are present in the asymmetric unit, giving a crystal volume per protein mass (VM) of 3.36,Å3,Da,1 and a solvent content of 63%. The diffraction limit of the crystals could be significantly extended by the crystal-annealing procedure. A set of native data extending to 2.7,Å resolution has been collected at 100,K using synchrotron X-rays. [source]