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Yorodumi- PDB-1jpu: Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jpu | ||||||
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Title | Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase | ||||||
Components | glycerol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / NAD / GLYCEROL METABOLISM | ||||||
Function / homology | Function and homology information anaerobic glycerol catabolic process / glycerol dehydrogenase (NAD+) activity / glycerol dehydrogenase / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å | ||||||
Authors | Ruzheinikov, S.N. / Burke, J. / Sedelnikova, S. / Baker, P.J. / Taylor, R. / Bullough, P.A. / Muir, N.M. / Gore, M.G. / Rice, D.W. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Glycerol dehydrogenase. structure, specificity, and mechanism of a family III polyol dehydrogenase. Authors: Ruzheinikov, S.N. / Burke, J. / Sedelnikova, S. / Baker, P.J. / Taylor, R. / Bullough, P.A. / Muir, N.M. / Gore, M.G. / Rice, D.W. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Purification, crystallization and quaternary structure analysis of a glycerol dehydrogenase S305C mutant from Bacillus stearothermophilus. Authors: Burke, J. / Ruzheinikov, S.N. / Sedelnikova, S. / Baker, P.J. / Holmes, D. / Muir, N.M. / Gore, M.G. / Rice, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jpu.cif.gz | 87.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jpu.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/1jpu ftp://data.pdbj.org/pub/pdb/validation_reports/jp/1jpu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a octamer generated from the monomer in the asymmetric unit by the operations: y, -x, z; -x, y, -z; x, -y, -z; y, x, -z; -x, -y, -z; -y, x, z and -y, -x, -z; |
-Components
#1: Protein | Mass: 39564.996 Da / Num. of mol.: 1 / Mutation: S305C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: GLDA or GLD / Plasmid: pKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM103 / References: UniProt: P32816, glycerol dehydrogenase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 48.08 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: Ammonum Sulfate, PEG 400, ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 30, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Num. all: 34428 / Num. obs: 34428 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.67 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.7 / % possible all: 83.4 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.8→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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