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- PDB-1p0c: Crystal Structure of the NADP(H)-Dependent Vertebrate Alcohol Deh... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p0c | ||||||
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Title | Crystal Structure of the NADP(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8) | ||||||
![]() | NADP-dependent ALCOHOL DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / ADH TOPOLOGY / NADP(H)-DEPENDENT | ||||||
Function / homology | ![]() alcohol dehydrogenase (NADP+) / alcohol dehydrogenase (NADP+) activity / alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) activity / retinol metabolic process / retinoic acid metabolic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Rana perezi (Iberian green frog) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rosell, A. / Valencia, E. / Pares, X. / Fita, I. / Farres, J. / Ochoa, W.F. | ||||||
![]() | ![]() Title: Crystal Structure of the Vertebrate NADP(H)-dependent Alcohol Dehydrogenase (ADH8) Authors: Rosell, A. / Valencia, E. / Pares, X. / Fita, I. / Farres, J. / Ochoa, W.F. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155 KB | Display | ![]() |
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PDB format | ![]() | 120.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.5 KB | Display | ![]() |
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Full document | ![]() | 466.3 KB | Display | |
Data in XML | ![]() | 31.4 KB | Display | |
Data in CIF | ![]() | 44.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39243.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rana perezi (Iberian green frog) / Gene: ADH / Plasmid: pGEX4T-2 / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.21 % | |||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, LiSO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | |||||||||||||||
Crystal grow | *PLUS Temperature: 293 KDetails: Valencia, E., (2003) Acta Crystallogr., Sect.D, 59, 334. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 79197 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection | *PLUS Num. measured all: 150436 / Rmerge(I) obs: 0.113 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / % possible obs: 99 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.201 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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