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Yorodumi- PDB-1jq5: Bacillus Stearothermophilus Glycerol dehydrogenase complex with NAD+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jq5 | ||||||
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Title | Bacillus Stearothermophilus Glycerol dehydrogenase complex with NAD+ | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 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 stearothemophilus 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 | 1jq5.cif.gz | 92.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jq5.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/1jq5 ftp://data.pdbj.org/pub/pdb/validation_reports/jq/1jq5 | HTTPS FTP |
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-Related structure data
Related structure data | 1jpuSC 1jqaC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is an 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; -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: Chemical | ChemComp-NAD / | #4: 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: 2.57 Å3/Da / Density % sol: 52.12 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: Ammonium Sulfate, PEG 400, ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Burke, J., (2001) Acta Crystallogr., Sect.D, 57, 165. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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 29, 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: 1.7→10 Å / Num. all: 42016 / Num. obs: 42016 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.7→1.74 Å / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.7 / % possible all: 78.6 |
Reflection | *PLUS Num. measured all: 196167 |
Reflection shell | *PLUS % possible obs: 78.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JPU Resolution: 1.7→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 30.06 Å2 | |||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.151 | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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