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Yorodumi- PDB-1hf3: ATOMIC X-RAY STRUCTURE OF LIVER ALCOHOL DEHYDROGENASE CONTAINING ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hf3 | ||||||
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Title | ATOMIC X-RAY STRUCTURE OF LIVER ALCOHOL DEHYDROGENASE CONTAINING Cadmium and a hydroxide adduct to NADH | ||||||
Components | ALCOHOL DEHYDROGENASE E CHAIN | ||||||
Keywords | OXIDOREDUCTASE / OXIDOREDUCTASE(NAD(A)-CHOH(D)) | ||||||
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: 1.95 Å | ||||||
Authors | Meijers, R. / Morris, R.J. / Adolph, H.W. / Merli, A. / Lamzin, V.S. / Cedergen-Zeppezauer, E.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: On the Enzymatic Activation of Nadh Authors: Meijers, R. / Morris, R.J. / Adolph, H.W. / Merli, A. / Lamzin, V.S. / Cedergen-Zeppezauer, E.S. #1: Journal: Biochemistry / Year: 1999 Title: Substitutions in a Flexible Loop of Horse Liver Alcohol Dehydrogenase Hinder the Conformational Change and Unmask Hydrogen Transfer Authors: Ramaswamy, S. / Park, D.H. / Plapp, B.V. #2: Journal: Biochemistry / Year: 1997 Title: Electrostatic Effects in the Kinetics of Coenzyme Binding to Isozymes of Alcohol Dehydrogenase from Horse Liver Authors: Adolph, H.W. / Kiefer, M. / Cedergren-Zeppezauer, E.S. #3: Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: Refined Crystal Structure of Liver Deresolutionhydrogenase-Nadh Complex at 1.8 Angstrom Alcohol Authors: Al-Karadaghi, S. / Cedergren-Zeppezauer, E.S. / Petratos, K. / Hovmoeller, S. / Terry, H. / Dauter, Z. / Wilson, K.S. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983 Title: Crystal Structures of the Active Site Inspecifically Metal-Depleted and Cobalt-Substituted Horse Liver Alcohol Dehydrogenase Derivatives Authors: Schneider, G. / Eklund, H. / Cedergren-Zeppezauer, E. / Zeppezauer, M. #5: Journal: Biochemistry / Year: 1983 Title: Crystal-Structure Determination of Reducnicotinamide Adenine Dinucleotide Complex with Horse Liver Alcohol Dehydrogenase Maintained in its Apo Conformation by Zinc-Bound Imidazoleed Authors: Cedergren-Zeppezauer, E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hf3.cif.gz | 168.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hf3.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 1hf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/1hf3 ftp://data.pdbj.org/pub/pdb/validation_reports/hf/1hf3 | HTTPS FTP |
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-Related structure data
Related structure data | 1hetC 1heuC 2ohxS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.12925, 0.98584, -0.10681), Vector: Details | BIOLOGICAL_UNIT: DIMERIC | |
-Components
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: ADDUCT BETWEEN NC6 OF NADH AND ZINC BOUND HYDROXIDE Source: (natural) EQUUS CABALLUS (horse) / References: UniProt: P00327, alcohol dehydrogenase #2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ALCOHOL + NAD(+) = ALDEHYDE OR KETONE + NADH. REQUIRES ZINC FOR ITS ACTIVITY. DIMER OF IDENTICAL OR ...ALCOHOL + NAD(+) = ALDEHYDE OR KETONE + NADH. REQUIRES ZINC FOR ITS ACTIVITY. DIMER OF IDENTICAL OR NONIDENTIC | |
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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: 2.37 Å3/Da / Density % sol: 48.19 % | ||||||||||||||||||
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Crystal grow | pH: 8.2 / Details: pH 8.20 | ||||||||||||||||||
Crystal grow | *PLUS Method: microdialysis | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.927 |
Detector | Type: MARRESEARCH X-RAY RESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.927 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→15 Å / Num. obs: 94521 / % possible obs: 86.6 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.95→2 Å / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.1 / % possible all: 69.8 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. obs: 45721 / Num. measured all: 94521 / Rmerge(I) obs: 0.037 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OHX Resolution: 1.95→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2
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Refinement step | Cycle: LAST / Resolution: 1.95→15 Å
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Refine LS restraints |
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