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Yorodumi- PDB-1d1t: MUTANT OF HUMAN SIGMA ALCOHOL DEHYDROGENASE WITH LEUCINE AT POSIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d1t | ||||||
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Title | MUTANT OF HUMAN SIGMA ALCOHOL DEHYDROGENASE WITH LEUCINE AT POSITION 141 | ||||||
Components | ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN | ||||||
Keywords | OXIDOREDUCTASE / ROSSMANN OR DINUCLEOTIDE FOLD | ||||||
Function / homology | Function and homology information omega-hydroxydecanoate dehydrogenase / omega-hydroxydecanoate dehydrogenase activity / ethanol binding / aldehyde oxidase activity / all-trans-retinol dehydrogenase (NAD+) / fatty acid omega-oxidation / receptor antagonist activity / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase (NAD+) activity, zinc-dependent ...omega-hydroxydecanoate dehydrogenase / omega-hydroxydecanoate dehydrogenase activity / ethanol binding / aldehyde oxidase activity / all-trans-retinol dehydrogenase (NAD+) / fatty acid omega-oxidation / receptor antagonist activity / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / retinoid metabolic process / retinol binding / response to bacterium / response to ethanol / zinc ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Xie, P.T. / Hurley, T.D. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: Methionine-141 directly influences the binding of 4-methylpyrazole in human sigma sigma alcohol dehydrogenase. Authors: Xie, P.T. / Hurley, T.D. #1: Journal: J.Biol.Chem. / Year: 1997 Title: X-ray structure of human class IV sigma-sigma alcohol dehydrogenase Authors: Xie, P.T. / Parsons, S.H. / Speckhard, D.C. / Bosron, W.F. / Hurley, T.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d1t.cif.gz | 301.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d1t.ent.gz | 244.7 KB | Display | PDB format |
PDBx/mmJSON format | 1d1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/1d1t ftp://data.pdbj.org/pub/pdb/validation_reports/d1/1d1t | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 39906.312 Da / Num. of mol.: 4 / Mutation: M141L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P40394, alcohol dehydrogenase |
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-Non-polymers , 5 types, 412 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-CAC / #5: Chemical | ChemComp-NAD / #6: Water | ChemComp-HOH / | |
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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: 2.88 Å3/Da / Density % sol: 57.25 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM Cacodylate, pH 6.5, 100 mM Zinc Acetate, 7.5 mM NAD+, 18% PEG 6000, 8 mg/ml enzyme, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 14, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 70587 / Num. obs: 64234 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.67 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.4→2.51 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.403 / Num. unique all: 8552 / % possible all: 77 |
Reflection | *PLUS Num. measured all: 171372 |
Reflection shell | *PLUS % possible obs: 77 % / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Resolution: 2.4→50 Å / σ(F): 0.5 / σ(I): 0.5 / Stereochemistry target values: Engh and Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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