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Yorodumi- PDB-5cdu: I220V horse liver alcohol dehydrogenase complexed with NAD and py... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cdu | ||||||
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Title | I220V horse liver alcohol dehydrogenase complexed with NAD and pyrazole | ||||||
Components | Alcohol dehydrogenase E chain | ||||||
Keywords | OXIDOREDUCTASE / alcohol / Rossmann fold | ||||||
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: 1.6 Å | ||||||
Authors | Plapp, B.V. / Shanmuganatham, K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2017 Title: Contribution of Buried Distal Amino Acid Residues in Horse Liver Alcohol Dehydrogenase to Structure and Catalysis. Authors: Shanmuganatham, K.K. / Wallace, R.S. / Lee, A.T. / 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 | 5cdu.cif.gz | 179.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cdu.ent.gz | 138.5 KB | Display | PDB format |
PDBx/mmJSON format | 5cdu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cdu_validation.pdf.gz | 992.9 KB | Display | wwPDB validaton report |
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Full document | 5cdu_full_validation.pdf.gz | 999.2 KB | Display | |
Data in XML | 5cdu_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 5cdu_validation.cif.gz | 58.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/5cdu ftp://data.pdbj.org/pub/pdb/validation_reports/cd/5cdu | HTTPS FTP |
-Related structure data
Related structure data | 5cdgC 5cdsC 5cdtC 5kj6C 5kjcC 5kjeC 5kjfC 4dwvS S: Starting model for refinement C: citing same article (ref.) |
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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: 39839.246 Da / Num. of mol.: 2 / Mutation: I220V Source method: isolated from a genetically manipulated source Details: I220V substitution in horse liver ADH1E / Source: (gene. exp.) Equus caballus (horse) / Organ: liver / Plasmid: pBPP/EqADH1E / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blu / References: UniProt: P00327, alcohol dehydrogenase |
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-Non-polymers , 5 types, 859 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: 48.53 % / Description: columns |
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 7 Details: 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL) METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA, 10 MG/ML PROTEIN, 1 MM NAD+, 10) MM PYRAZOLE, 16 TO 25 % 2-METHYL-2,4-PENTANEDIOL |
-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 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 89788 / % possible obs: 93.4 % / Redundancy: 6.46 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 0.414 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 6.13 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.9 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DWV Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.888 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.272 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→20 Å
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Refine LS restraints |
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