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- PDB-1jqa: Bacillus stearothermophilus glycerol dehydrogenase complex with g... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jqa | ||||||
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Title | Bacillus stearothermophilus glycerol dehydrogenase complex with glycerol | ||||||
![]() | Glycerol Dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / NAD / Glycerol metabolism | ||||||
Function / homology | ![]() anaerobic glycerol catabolic process / glycerol dehydrogenase (NAD+) activity / glycerol dehydrogenase / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ruzheinikov, S.N. / Burke, J. / Sedelnikova, S. / Baker, P.J. / Taylor, R. / Bullough, P.A. / Muir, N.M. / Gore, M.G. / Rice, D.W. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86 KB | Display | ![]() |
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PDB format | ![]() | 64.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 377.3 KB | Display | ![]() |
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Full document | ![]() | 379.9 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 13.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jpuSC ![]() 1jq5C C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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 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; |
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Components
#1: Protein | Mass: 39564.996 Da / Num. of mol.: 1 / Mutation: S305C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: GLDA or GLD / Plasmid: pKK233-2 / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.56 % |
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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 |
-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→10 Å / Num. all: 25033 / Num. obs: 25033 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.05→2.1 Å / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 2.9 / % possible all: 72 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JPU Resolution: 2.05→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: 36.55 Å2 | |||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→10 Å
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Refine LS restraints |
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