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Yorodumi- PDB-1ykf: NADP-DEPENDENT ALCOHOL DEHYDROGENASE FROM THERMOANAEROBIUM BROCKII -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ykf | ||||||
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Title | NADP-DEPENDENT ALCOHOL DEHYDROGENASE FROM THERMOANAEROBIUM BROCKII | ||||||
Components | NADP-DEPENDENT ALCOHOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information isopropanol dehydrogenase (NADP+) / isopropanol dehydrogenase (NADP+) activity / zinc ion binding Similarity search - Function | ||||||
Biological species | Thermoanaerobacter brockii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Korkhin, Y. / Frolow, F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: NADP-dependent bacterial alcohol dehydrogenases: crystal structure, cofactor-binding and cofactor specificity of the ADHs of Clostridium beijerinckii and Thermoanaerobacter brockii. Authors: Korkhin, Y. / Kalb(Gilboa), A.J. / Peretz, M. / Bogin, O. / Burstein, Y. / Frolow, F. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Crystalline Alcohol Dehydrogenases from the Mesophilic Bacterium Clostridium Beijerinckii and the Thermophilic Bacterium Thermoanaerobium Brockii: Preparation, Characterization and Molecular Symmetry Authors: Korkhin, Y. / Frolow, F. / Bogin, O. / Peretz, M. / Kalb(Gilboa), A.J. / Burstein, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ykf.cif.gz | 270.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ykf.ent.gz | 221.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ykf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/1ykf ftp://data.pdbj.org/pub/pdb/validation_reports/yk/1ykf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 37694.871 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: HOLO-ENZYME FORM / Source: (gene. exp.) Thermoanaerobacter brockii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P14941, alcohol dehydrogenase (NADP+) #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 32 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.2 / Details: pH 8.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 8.3 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Apr 27, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→33 Å / Num. obs: 44669 / % possible obs: 88.4 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 1.93 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 4.3 / % possible all: 75.8 |
Reflection shell | *PLUS % possible obs: 75.8 % / Num. unique obs: 2547 |
-Processing
Software |
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Refinement | Resolution: 2.5→8 Å / σ(F): 0
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Displacement parameters | Biso mean: 36.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 44669 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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