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Yorodumi- PDB-6cy3: Horse liver E267N alcohol dehydrogenase complex with 3'-dephospho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cy3 | ||||||
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Title | Horse liver E267N alcohol dehydrogenase complex with 3'-dephosphocoenzyme A | ||||||
Components | alcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / NAD-dependent horse liver alcohol dehydrogenase E267N mutant 3'-dephosphocoenzyme A | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Plapp, B.V. | ||||||
Funding support | United States, 1items
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Citation | Journal: Arch. Biochem. Biophys. / Year: 2018 Title: Substitutions of a buried glutamate residue hinder the conformational change in horse liver alcohol dehydrogenase and yield a surprising complex with endogenous 3'-Dephosphocoenzyme A. Authors: Kim, Y.H. / Gogerty, D.S. / 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 | 6cy3.cif.gz | 87.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cy3.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 6cy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cy3_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6cy3_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6cy3_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 6cy3_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/6cy3 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/6cy3 | HTTPS FTP |
-Related structure data
Related structure data | 6cxxC 1qlhS 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
#1: Protein | Mass: 39838.262 Da / Num. of mol.: 1 / Mutation: E267N Source method: isolated from a genetically manipulated source Source: (gene. exp.) EQUUS CABALLUS (horse) / Organ: liver / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P00327 | ||||
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#2: Chemical | #3: Chemical | ChemComp-COD / | #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: 2.35 Å3/Da / Density % sol: 47.7 % / Description: needles |
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Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 8.4 Details: 10 mtg/ml enzyme dialyzed against 50 mM tris(hydroxymethyl)aminomethane-HCl, 0.25 mM EDTA, containing 2-methy-2,4-pentanediol increasing to 25 %. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 12, 2004 / Details: MSC YALE CONFOCAL OSMIC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→20 Å / Num. obs: 14923 / % possible obs: 87.1 % / Redundancy: 4.97 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.042 / Rrim(I) all: 0.091 / Χ2: 1.18 / Net I/av σ(I): 12.4 / Net I/σ(I): 12.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1qlh Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.906 / SU B: 14.677 / SU ML: 0.315 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.685 / ESU R Free: 0.359 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.33 Å2 / Biso mean: 53.912 Å2 / Biso min: 28.32 Å2
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Refinement step | Cycle: final / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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