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Yorodumi- PDB-2jhg: Structural evidence for a ligand coordination switch in liver alc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jhg | ||||||
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Title | Structural evidence for a ligand coordination switch in liver alcohol dehydrogenase | ||||||
Components | ALCOHOL DEHYDROGENASE E CHAIN | ||||||
Keywords | OXIDOREDUCTASE / METAL COORDINATION / NAD / ZINC / INHIBITION / ACETYLATION / METAL-BINDING / ALCOHOL DEHYDROGENASE | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / 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 | Meijers, R. / Adolph, H.W. / Dauter, Z. / Wilson, K.S. / Lamzin, V.S. / Cedergren-Zeppezauer, E.S. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Structural Evidence for a Ligand Coordination Switch in Liver Alcohol Dehydrogenase Authors: Meijers, R. / Adolph, H.W. / Dauter, Z. / Wilson, K.S. / Lamzin, V.S. / Cedergren-Zeppezauer, E.S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jhg.cif.gz | 367.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jhg.ent.gz | 301.5 KB | Display | PDB format |
PDBx/mmJSON format | 2jhg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jhg_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2jhg_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2jhg_validation.xml.gz | 45.3 KB | Display | |
Data in CIF | 2jhg_validation.cif.gz | 71.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/2jhg ftp://data.pdbj.org/pub/pdb/validation_reports/jh/2jhg | HTTPS FTP |
-Related structure data
Related structure data | 2jhfC 1hetS 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
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: HORSE LIVER / Source: (natural) EQUUS CABALLUS (horse) / Organ: LIVER / Variant: HORSE LIVER / References: UniProt: P00327, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: 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: 2.2 Å3/Da / Density % sol: 45 % |
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Crystal grow | Details: DIALYSIS 30 MM TRIS/HCL PH 8.2 25 % MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→25 Å / Num. obs: 212570 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.2→1.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.8 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HET Resolution: 1.2→19.83 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.05 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ADDUCT BETWEEN ISOBUTYRAMIDE AND THE C4 ATOM ON THE PYRIDINE RING OF NADH
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→19.83 Å
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Refine LS restraints |
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