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Yorodumi- PDB-1e3l: P47H mutant of mouse class II alcohol dehydrogenase complex with NADH -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e3l | ||||||
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Title | P47H mutant of mouse class II alcohol dehydrogenase complex with NADH | ||||||
Components | ALCOHOL DEHYDROGENASE, CLASS II | ||||||
Keywords | ALCOHOL DEHYDROGENASE | ||||||
Function / homology | Function and homology information benzaldehyde dehydrogenase [NAD(P)+] activity / Ethanol oxidation / alcohol catabolic process / RA biosynthesis pathway / quinone metabolic process / ethanol binding / ethanol metabolic process / all-trans-retinol dehydrogenase (NAD+) / all-trans retinal binding / S-(hydroxymethyl)glutathione dehydrogenase (NAD(P)+) activity ...benzaldehyde dehydrogenase [NAD(P)+] activity / Ethanol oxidation / alcohol catabolic process / RA biosynthesis pathway / quinone metabolic process / ethanol binding / ethanol metabolic process / all-trans-retinol dehydrogenase (NAD+) / all-trans retinal binding / S-(hydroxymethyl)glutathione dehydrogenase (NAD(P)+) activity / fatty acid omega-oxidation / NADPH:quinone reductase activity / alcohol metabolic process / formaldehyde catabolic process / cellular aldehyde metabolic process / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / all-trans-retinol dehydrogenase (NAD+) activity / aldose reductase (NADPH) activity / retinol metabolic process / retinoid metabolic process / retinol binding / NAD binding / zinc ion binding / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Svensson, S. / Hoog, J.O. / Schneider, G. / Sandalova, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal Structure of Mouse Class II Alcohol Dehydrogenase Reveal Determinants of Substrate Specificity and Catalytic Efficiency Authors: Svensson, S. / Hoeoeg, J.O. / Schneider, G. / Sandalova, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e3l.cif.gz | 154.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e3l.ent.gz | 121.9 KB | Display | PDB format |
PDBx/mmJSON format | 1e3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/1e3l ftp://data.pdbj.org/pub/pdb/validation_reports/e3/1e3l | HTTPS FTP |
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-Related structure data
Related structure data | 1e3eC 1e3iC 1cdoS 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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-Components
#1: Protein | Mass: 40135.445 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cellular location: CYTOSOLICCytosol / Organ: LIVER / Plasmid: PET29 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9QYY9, alcohol dehydrogenase #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Compound details | CHAIN A, B ENGINEERED | |
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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: 2.04 Å3/Da / Density % sol: 39.79 % | |||||||||||||||||||||||||
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Crystal grow | pH: 8.3 / Details: pH 8.30 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.032 |
Detector | Type: MARRESEARCH / Date: Jan 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.032 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. obs: 22033 / % possible obs: 99 % / Redundancy: 3.1 % / Rsym value: 0.068 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.5→2.55 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.321 / % possible all: 94 |
Reflection | *PLUS % possible obs: 99 % / Num. measured all: 68302 / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS % possible obs: 94.7 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 7.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CDO Resolution: 2.5→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 37.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→25 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2598 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.327 / Rfactor obs: 0.245 |