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Matthews Coefficient Calculations (Matthew + coefficient_calculation)
Selected AbstractsCrystallization and preliminary X-ray crystallographic analysis of l -rhamnose isomerase with a novel high thermostability from Bacillus haloduransACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2010Thi-Ngoc-Thanh Doan l -Rhamnose isomerases catalyze isomerization between l -rhamnose (6-deoxy- l -mannose) and l -rhamnulose (6-deoxy- l -fructose), which is the first step in rhamnose catabolism. l -Rhamnose isomerase from Bacillus halodurans ATCC BAA-125 (BHRI) exhibits interesting characteristics such as high thermostability and selective substrate specificity. BHRI fused with an HHHHHH sequence was purified and crystallized in order to elucidate the molecular basis of its unique enzymatic properties. The crystals were grown by the hanging-drop vapour-diffusion method and belonged to the monoclinic space group P21, with unit-cell parameters a = 83.2, b = 164.9, c = 92.0,Å, , = 116.0°. Diffraction data were collected to 2.5,Å resolution. According to a Matthews coefficient calculation, there are four monomers in the asymmetric unit with a VM of 3.0,Å3,Da,1 and a solvent content of 59.3%. The initial structure of BHRI has been determined by the molecular-replacement method. [source] Complex assembly, crystallization and preliminary X-ray crystallographic studies of duck MHC class I moleculeACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2010Jianhua Zhang In order to understand the biological properties of the immune systems of waterfowl and to establish a system for structural studies of duck class I major histocompatibility complex (DuMHC I), a complex of DuMHC I with duck ,2 -microglobulin (Du,2m) and the peptide AEIEDLIF (AF8) derived from H5N1 NP residues 251,258 was assembled. The complex was crystallized; the crystals belonged to space group C2221, with unit-cell parameters a = 54.7, b = 72.4, c = 102.2,Å, and diffracted to 2.3,Å resolution. Matthews coefficient calculation and initial structure determination by molecular replacement showed that the crystals did not contain the whole DuMHC I complex, but instead contained the DuMHC I ,3 domain and a Du,2m molecule (DuMHC I ,3+,2m). Another complex of DuMHC I with the peptide IDWFDGKE derived from a chicken fusion protein also generated the same results. The stable structure of DuMHC I ,3+,2m may reflect some unique characteristics of DuMHC I and pave the way for novel MHC structure-related studies in the future. [source] Crystallization and preliminary analysis of a water-forming NADH oxidase from Lactobacillus sanfranciscensisACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2004George T. Lountos Single crystals have been obtained of NADH oxidase (Nox), a flavoenzyme cloned from Lactobacillus sanfranciscensis. The enzyme catalyzes the oxidation of two equivalents of NAD(P)H and reduces one equivalent of oxygen to yield two equivalents of water, without releasing hydrogen peroxide after the reduction of the first equivalent of NAD(P)H. The enzyme crystallizes in space group P212121, with unit-cell parameters a = 59.6, b = 92.6, c = 163.5,Å. The crystals diffract to 1.85,Å resolution using synchrotron radiation. Matthews coefficient calculations suggest the presence of two molecules per asymmetric unit (VM = 2.3,Å3,Da,1, 45.5% solvent content), which has been confirmed by the molecular-replacement solution using a search molecule derived from NADH peroxidase (PDB code 1f8w). [source] Expression, crystallization and preliminary X-ray crystallographic studies of Arthrobacter globiformis inulin fructotransferaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2003Mitsuru Momma A recombinant form of Arthrobacter globiformis inulin fructotransferase (DFAIII-producing) has been overexpressed in Escherichia coli and purified to homogeneity. Crystals were obtained at 293,K by the hanging-drop vapour-diffusion technique using 0.1,M Na HEPES pH 7.5 buffer containing 1.5,M lithium sulfate as a precipitant. Crystals of the recombinant wild-type enzyme diffracted to better than 1.5,Å at 100,K using a synchrotron-radiation source at the Photon Factory. The crystal belonged to space group R32, with unit-cell parameters a = b = 92.02, c = 229.82,Å in the hexagonal axes. Assuming the presence of one molecule in the asymmetric unit, the VM value for the crystal was 2.15,Å3,Da,1, indicating a solvent content of 42.8%. Selenomethionine-derivative crystals belonged to a different space group, C2, with unit-cell parameters a = 159.32, b = 91.92, c = 92.58,Å, , = 125.06. Matthews coefficient calculations suggested that the C2 selenomethionine-derivative crystal contained three molecules per asymmetric unit. [source] Overexpression, crystallization and preliminary X-ray crystallographic analysis of d -ribose-5-phosphate isomerase from Clostridium thermocellumACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 11 2009Junho Jung Rare sugars are used for many industrial and medical purposes and are produced by the interconversion between aldoses and ketoses catalyzed by sugar and sugar-phosphate isomerases. Recently, Clostridium thermocellumd -ribose-5-phosphate isomerase (CTRPI), an aldose,ketose isomerase, was cloned in order to synthesize d -allose and its substrate specificity was further characterized for industrial usage. CTRPI has a novel substrate specificity that differs from those of other isomerases, which have broad substrate specificities. CTRPI prefers aldose substrates such as l -talose, d -ribose and d -allose. CTRPI was purified and crystallized in order to determine its three-dimensional structure and thus to elucidate its enzymatic reaction mechanism and understand its substrate specificity. The crystal belonged to the trigonal space group P3221, with unit-cell parameters a = b = 69.5, c = 154.4,Å, and diffracted to 1.9,Å resolution. According to Matthews coefficient calculations, the crystallographic structure consists of a dimer in the asymmetric unit, with a VM of 3.2,Å3,Da,1 and a solvent content of 61.7%. [source] Cloning, purification and preliminary X-ray analysis of the C-terminal domain of Helicobacter pylori MotBACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2008Anna Roujeinikova The C-terminal domain of MotB (MotB-C) contains a putative peptidoglycan-binding motif and is believed to anchor the MotA/MotB stator unit of the bacterial flagellar motor to the cell wall. Crystals of Helicobacter pylori MotB-C (138 amino-acid residues) were obtained by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitant. These crystals belong to space group P21, with unit-cell parameters a = 50.8, b = 89.5, c = 66.3,Å, , = 112.5°. The crystals diffract X-rays to at least 1.6,Å resolution using a synchrotron-radiation source. Self-rotation function and Matthews coefficient calculations suggest that the asymmetric unit contains one tetramer with 222 point-group symmetry. The anomalous difference Patterson maps calculated for an ytterbium-derivative crystal using diffraction data at a wavelength of 1.38,Å showed significant peaks on the v = 1/2 Harker section, suggesting that ab initio phase information could be derived from the MAD data. [source] | ||||||||||