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Yorodumi- PDB-1ps0: Crystal Structure of the NADP(H)-Dependent Cinnamyl Alcohol Dehyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ps0 | ||||||
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Title | Crystal Structure of the NADP(H)-Dependent Cinnamyl Alcohol Dehydrogenase from Saccharomyces cerevisiae | ||||||
Components | Hypothetical zinc-type alcohol dehydrogenase-like protein in PRE5-FET4 intergenic region | ||||||
Keywords | OXIDOREDUCTASE / ADH TOPOLOGY / NADP(H)DEPENDENT | ||||||
Function / homology | Function and homology information hydroxymethylfurfural reductase (NADH) activity / hydroxymethylfurfural reductase (NADPH) activity / furaldehyde metabolic process / 3-methylbutanal reductase (NADPH) activity / cinnamyl-alcohol dehydrogenase activity / alcohol dehydrogenase (NADP+) / alcohol metabolic process / alcohol dehydrogenase (NADP+) activity / cellular aldehyde metabolic process / zinc ion binding ...hydroxymethylfurfural reductase (NADH) activity / hydroxymethylfurfural reductase (NADPH) activity / furaldehyde metabolic process / 3-methylbutanal reductase (NADPH) activity / cinnamyl-alcohol dehydrogenase activity / alcohol dehydrogenase (NADP+) / alcohol metabolic process / alcohol dehydrogenase (NADP+) activity / cellular aldehyde metabolic process / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Valencia, E. / Larroy, C. / Ochoa, W.F. / Pares, X. / Fita, I. / Biosca, J.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Apo and Holo Structures of an NADP(H)-dependent Cinnamyl Alcohol Dehydrogenase from Saccharomyces cerevisiae Authors: Valencia, E. / Larroy, C. / Ochoa, W.F. / Pares, X. / Fita, I. / Biosca, J.A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallization and preliminary X-ray analysis of NADP(H)-dependent alcohol dehydrogenases from Saccharomyces cerevisiae and Rana perezi Authors: Valencia, E. / Rosell, A. / Larroy, C. / Farres, J. / Biosca, J.A. / Fita, I. / Pares, X. / Ochoa, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ps0.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ps0.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ps0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/1ps0 ftp://data.pdbj.org/pub/pdb/validation_reports/ps/1ps0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer generated by the crystallographic two fold axis: x, y, -z. |
-Components
#1: Protein | Mass: 39669.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YMR318C (ADH6) / Plasmid: PYES2-YMR318C / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ2168 / References: UniProt: Q04894 | ||
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#2: Chemical | #3: Chemical | ChemComp-NAP / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.68 Å3/Da / Density % sol: 78.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 19, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. all: 18496 / Num. obs: 18395 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.072 / Rsym value: 0.086 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→5 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.01→5 Å
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Xplor file |
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