+Open data
-Basic information
Entry | Database: PDB / ID: 1geg | ||||||
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Title | CRYATAL STRUCTURE ANALYSIS OF MESO-2,3-BUTANEDIOL DEHYDROGENASE | ||||||
Components | ACETOIN REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / SDR FAMILY | ||||||
Function / homology | Function and homology information diacetyl reductase [(S)-acetoin forming] / diacetyl reductase ((S)-acetoin forming) activity / acetoin catabolic process Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Otagiri, M. / Kurisu, G. / Ui, S. / Kusunoki, M. | ||||||
Citation | Journal: J.Biochem. / Year: 2001 Title: Crystal structure of meso-2,3-butanediol dehydrogenase in a complex with NAD+ and inhibitor mercaptoethanol at 1.7 A resolution for understanding of chiral substrate recognition mechanisms. Authors: Otagiri, M. / Kurisu, G. / Ui, S. / Takusagawa, Y. / Ohkuma, M. / Kudo, T. / Kusunoki, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1geg.cif.gz | 388.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1geg.ent.gz | 319.6 KB | Display | PDB format |
PDBx/mmJSON format | 1geg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/1geg ftp://data.pdbj.org/pub/pdb/validation_reports/ge/1geg | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
-Protein / Sugars , 2 types, 16 molecules ABCDEFGH
#1: Protein | Mass: 26618.299 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Plasmid: PUC119 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q48436, acetoin dehydrogenase #2: Sugar | ChemComp-GLC / |
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-Non-polymers , 4 types, 859 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-NAD / #5: Chemical | ChemComp-BME / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 6000, 100mM HEPES, magnesium chloride, glucose, 2-mercaptoethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. all: 203543 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.192 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 203217 / % possible obs: 100 % |
Reflection shell | *PLUS Highest resolution: 1.7 Å / % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.7→40 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 40 Å / σ(F): 2 / Rfactor obs: 0.193 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS
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