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Yorodumi- PDB-1u3w: Crystal Structure of Human Alcohol Dehydrogenase Gamma-2-Gamma-2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u3w | ||||||
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Title | Crystal Structure of Human Alcohol Dehydrogenase Gamma-2-Gamma-2 Isoform Complexed with N-1-Methylheptylformamide Determined to 1.45 Angstrom Resolution | ||||||
Components | Alcohol dehydrogenase gamma chain | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information Ethanol oxidation / RA biosynthesis pathway / alcohol dehydrogenase (NAD+) activity / : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / nucleoplasm ...Ethanol oxidation / RA biosynthesis pathway / alcohol dehydrogenase (NAD+) activity / : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / nucleoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Gibbons, B.J. / Hurley, T.D. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Structure of three class I human alcohol dehydrogenases complexed with isoenzyme specific formamide inhibitors Authors: Gibbons, B.J. / Hurley, T.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u3w.cif.gz | 173.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u3w.ent.gz | 135.4 KB | Display | PDB format |
PDBx/mmJSON format | 1u3w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u3w_validation.pdf.gz | 984.6 KB | Display | wwPDB validaton report |
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Full document | 1u3w_full_validation.pdf.gz | 996.3 KB | Display | |
Data in XML | 1u3w_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 1u3w_validation.cif.gz | 58.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/1u3w ftp://data.pdbj.org/pub/pdb/validation_reports/u3/1u3w | HTTPS FTP |
-Related structure data
Related structure data | 1u3tC 1u3uC 1u3vC 1ht0S 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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Details | The assymetric unit contains one homodimer. |
-Components
#1: Protein | Mass: 39743.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADH1C / Plasmid: pKK2233 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha / References: UniProt: P00326, 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: 2.1 Å3/Da / Density % sol: 40.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 10mg/ml enzyme, 4mM NAD+, 50mM Tris-HCl, and 17-19% PEG 6000, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2001 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.2→29.36 Å / Num. all: 110343 / Num. obs: 110343 / % possible obs: 62.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.45→1.488 Å / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.1 / Num. unique all: 8042 / % possible all: 98.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HT0 Resolution: 1.45→29.36 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.699 / SU ML: 0.061 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.075 / ESU R Free: 0.075 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.028 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→29.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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