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Yorodumi- PDB-3oq6: Horse liver alcohol dehydrogenase A317C mutant complexed with NAD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oq6 | ||||||
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Title | Horse liver alcohol dehydrogenase A317C mutant complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol | ||||||
Components | Alcohol dehydrogenase E chain | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / alcohol metabolism / NAD | ||||||
Function / homology | Function and homology information : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinol metabolic process / retinoic acid metabolic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Plapp, B.V. / Herdendorf, T.J. | ||||||
Citation | Journal: Chem.Biol.Interact / Year: 2011 Title: Origins of the high catalytic activity of human alcohol dehydrogenase 4 studied with horse liver A317C alcohol dehydrogenase. Authors: Herdendorf, T.J. / Plapp, B.V. #1: Journal: Biochemistry / Year: 1994 Title: Structures of horse liver alcohol dehydrogenase complexed with NAD and substituted benzyl alcohols Authors: Ramaswamy, S. / Eklund, H. / Plapp, B.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oq6.cif.gz | 348.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oq6.ent.gz | 283.2 KB | Display | PDB format |
PDBx/mmJSON format | 3oq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oq6_validation.pdf.gz | 985.2 KB | Display | wwPDB validaton report |
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Full document | 3oq6_full_validation.pdf.gz | 989.6 KB | Display | |
Data in XML | 3oq6_validation.xml.gz | 40 KB | Display | |
Data in CIF | 3oq6_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/3oq6 ftp://data.pdbj.org/pub/pdb/validation_reports/oq/3oq6 | HTTPS FTP |
-Related structure data
Related structure data | 1hldS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39885.336 Da / Num. of mol.: 2 / Mutation: A317C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: ADH E / Plasmid: pET23d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(lamdaDE3) / References: UniProt: P00327, alcohol dehydrogenase |
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-Non-polymers , 5 types, 1109 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | #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: 2.39 Å3/Da / Density % sol: 48.51 % |
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 7 Details: 50 mM ammonium TES [N-tris(hydroxymethyl)-2-aminoethane sulfonate], 25% MRD, 11 mg/ml protein, 11 mM NAD+, 5 mM 2,3,4,5,6-pentafluorobenzyl alcohol, pH 7.0, MICRODIALYSIS, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: NOIR-1 / Detector: CCD / Date: Mar 27, 2009 / Details: SAGGITALLY FOCUSED MIRRORS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→90 Å / Num. obs: 214213 / % possible obs: 92.2 % / Redundancy: 3.57 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1 / Net I/σ(I): 9.4 / Scaling rejects: 5787 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1hld Resolution: 1.2→19.85 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.1748 / WRfactor Rwork: 0.1442 / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.8668 / SU B: 1.303 / SU ML: 0.026 / SU R Cruickshank DPI: 0.0359 / SU Rfree: 0.0362 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. B107 GLU O TOO CLOSE TO B741 O, BECAUSE OF A WOBBLE IN THE PEPTIDE BACKBONE THAT THE AUTHORS ARE UNABLE TO FIT PROPERLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.31 Å2 / Biso mean: 17.5778 Å2 / Biso min: 5.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→19.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.229 Å / Total num. of bins used: 20
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