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MAD Data Set (mad + data_set)

Distribution by Scientific Domains
Chemistry100%

Kinds of MAD Data Set

  • three-wavelength mad data set
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    Selected Abstracts

    Crystals of ternary protein,DNA complexes composed of DNA-binding domains of c-Myb or v-­Myb, C/EBP, or C/EBP, and tom-1A promoter fragment

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2001
    Tahir H. Tahirov
    c-Myb and the C/EBP family are transcriptional regulatory factors that act in concert to regulate the expression of myeloid-specific genes. v-Myb encoded by avian myeloblastosis virus (AMV) is a mutated form of c-Myb that contains point mutations which disrupt the cooperation with C/EBPs. To understand the mechanism of the transcriptional synergy between c-Myb and C/EBPs and the effect of the v-Myb mutations on that synergy, knowledge based on their three-dimensional structures is essential. Crystals of ternary complexes, in which various combinations of the DNA-binding domains of c-Myb or v-Myb and C/EBP, or C/EBP, are bound to a DNA fragment from tom-1A promoter, were obtained by the vapour-diffusion method. Complete diffraction data sets were obtained from each native crystal and two types of iodine-derivative crystals. A three-wavelength MAD data set was also obtained from a bromine-derivative crystal. [source]

    Purification, crystallization and preliminary X-ray diffraction analysis of the lytic transglycosylase MltF from Escherichia coli

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010
    Pramod K. Madoori
    The lytic transglycosylase MltF from Escherichia coli is an outer-membrane-bound periplasmic protein with two domains: a C-terminal catalytic domain with a lysozyme-like fold and an N-terminal domain of unknown function that is homologous to the periplasmic substrate-binding proteins of ABC transporters. In order to investigate its structure and function, a soluble form of full-length MltF (sMltF) containing both domains and a soluble fragment containing only the N-terminal domain (sMltF-NTD) were purified and crystallized. Crystals of sMltF belonged to space group P43212 or P41212, with unit-cell parameters a = b = 110.8, c = 163.5,Å and one or two molecules per asymmetric unit. A complete data set was collected to 3.5,Å resolution. Crystals of sMltF-NTD belonged to space group P3121, with unit-cell parameters a = b = 82.4, c = 75.2,Å and one molecule per asymmetric unit. For sMltF-NTD, a complete native data set was collected to 2.20,Å resolution. In addition, for phasing purposes, a three-wavelength MAD data set was collected to 2.5,Å resolution using a bromide-soaked sMltF-NTD crystal. Using phases derived from the Br-MAD data, it was possible to build a partial model of sMltF-NTD. [source]

    Purification, crystallization and preliminary X-ray analysis of a deletion mutant of a major buckwheat allergen

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2009
    Yuichiro Kezuka
    A 16,kDa buckwheat protein (BWp16) is a major allergen responsible for immediate hypersensitivity reactions including anaphylaxis. A deletion mutant of BWp16 (rBWp16,N) was overproduced and purified and was shown to be immunologically active. A three-wavelength MAD data set was collected from a crystal of selenomethionine-labelled rBWp16,N. The crystal belonged to the triclinic space group P1, with unit-cell parameters a = 28.39, b = 31.54, c = 32.20,Å, , = 111.92, , = 108.91, , = 98.74°. One monomer was expected to be present in the asymmetric unit based on the calculated Matthews coefficient of 1.76,Å3,Da,1. [source]

    Expression, crystallization and preliminary crystallographic analysis of PilZXAC1133 from Xanthomonas axonopodis pv. citri

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2009
    Cristiane R. Guzzo
    Proteins containing PilZ domains are widespread in Gram-negative bacteria and have recently been shown to be involved in the control of biofilm formation, adherence, aggregation, virulence-factor production and motility. Furthermore, some PilZ domains have recently been shown to bind the second messenger bis(3,,5,)cyclic diGMP. Here, the cloning, expression, purification and crystallization of PilZXAC1133, a protein consisting of a single PilZ domain from Xanthomonas axonopodis pv. citri, is reported. The closest PilZXAC1133 homologues in Pseudomonas aeruginosa and Neisseria meningitidis control type IV pilus function. Recombinant PilZXAC1133 containing selenomethionine was crystallized in space group P61. The unit-cell parameters were a = 62.125, b = 62.125, c = 83.543,Å. These crystals diffracted to 1.85,Å resolution and a MAD data set was collected at a synchrotron source. The calculated Matthews coefficient suggested the presence of two PilZXAC1133 molecules in the asymmetric unit. [source]

    Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of chlorite dismutase: a detoxifying enzyme producing molecular oxygen

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2008
    Daniël C. De Geus
    Chlorite dismutase, a homotetrameric haem-based protein, is one of the key enzymes of (per)chlorate-reducing bacteria. It is highly active (>2,kU,mg,1) in reducing the toxic compound chlorite to the innocuous chloride anion and molecular oxygen. Chlorite itself is produced as the intermediate product of (per)chlorate reduction. The chlorite dismutase gene in Azospira oryzae strain GR-1 employing degenerate primers has been identified and the active enzyme was subsequently overexpressed in Escherichia coli. Chlorite dismutase was purified, proven to be active and crystallized using sitting drops with PEG 2000 MME, KSCN and ammonium sulfate as precipitants. The crystals belonged to space group P21212 and were most likely to contain six subunits in the asymmetric unit. The refined unit-cell parameters were a = 164.46, b = 169.34, c = 60.79,Å. The crystals diffracted X-rays to 2.1,Å resolution on a synchrotron-radiation source and a three-wavelength MAD data set has been collected. Determination of the chlorite dismutase structure will provide insights into the active site of the enzyme, for which no structures are currently available. [source]

    Purification, crystallization and preliminary X-ray diffraction analysis of the putative ABC transporter ATP-binding protein from Thermotoga maritima

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2008
    Abdul S. Ethayathulla
    Adenosine triphosphate (ATP) binding cassette transporters (ABC transporters) are ATP hydrolysis-dependent transmembrane transporters. Here, the overproduction, purification and crystallization of the putative ABC transporter ATP-binding protein TM0222 from Thermotoga maritima are reported. The protein was crystallized in the hexagonal space group P6422, with unit-cell parameters a = b = 148.49, c = 106.96,Å, , = 120.0°. Assuming the presence of two molecules in the asymmetric unit, the calculated VM is 2.84,Å3,Da,1, which corresponds to a solvent content of 56.6%. A three-wavelength MAD data set was collected to 2.3,Å resolution from SeMet-substituted TM0222 crystals. Data sets were collected on the BL38B1 beamline at SPring-8, Japan. [source]

    Overexpression, purification, crystallization and preliminary X-ray cystallographic studies of a proline-specific aminopeptidase from Aneurinibacillus sp. strain AM-1

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2006
    Makoto Akioka
    To elucidate the structure and molecular mechanism of a characteristic proline-specific aminopeptidase produced by the thermophile Aneurinibacillus sp. strain AM-1, its gene was cloned and the recombinant protein was overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 1.8,Å resolution from the recombinant aminopeptidase crystal. The crystals belong to the orthorhombic space group P21212, with unit-cell parameters a = 93.62, b = 68.20, c = 76.84,Å. A complete data set was also obtained from crystals of SeMet-substituted aminopeptidase. Data in the resolution range 20,2.1,Å from the MAD data set from the SeMet-substituted crystal were used for phase determination. [source]

    Preliminary crystallographic analysis of the Escherichia coli YeaZ protein using the anomalous signal of a gadolinium derivative

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2005
    Richard Kahn
    The Escherichia coli yeaZ gene encodes a 231-residue protein (Mr = 25,180) that belongs to a family of proteins that are conserved in various bacterial genomes. This protein of unknown function is predicted to be a hypothetical protease. The YeaZ protein was overexpressed in E. coli and crystallized at 298,K by the hanging-drop vapour-diffusion method. A MAD data set was collected using a gadolinium-derivative crystal that had been soaked with 0.1,M Gd-DOTMA. The data set contained data collected to a resolution of 2.7,Å at two wavelengths at the LIII absorption edge of gadolinium, while remote data were collected to a resolution of 2.28,Å. The crystal belonged to the orthorhombic space group P212121, with unit-cell parameters a = 76.3, b = 97.6, c = 141.9,Å. Phasing using the MAD method confirmed there to be four monomers in the asymmetric unit related by two twofold axes as identified by the self-rotation function search. [source]