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Yorodumi- PDB-1a71: TERNARY COMPLEX OF AN ACTIVE SITE DOUBLE MUTANT OF HORSE LIVER AL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a71 | ||||||
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Title | TERNARY COMPLEX OF AN ACTIVE SITE DOUBLE MUTANT OF HORSE LIVER ALCOHOL DEHYDROGENASE, PHE93=>TRP, VAL203=>ALA WITH NAD AND TRIFLUOROETHANOL | ||||||
Components | LIVER ALCOHOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / OXIDOREDUCTASE (NAD(A)-CHOH(D)) / LIVER / ALCOHOL / DEHYDROGENASE / LADH / ACTIVE SITE MUTANT | ||||||
Function / homology | Function and homology information : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinol metabolic process / retinoic acid metabolic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Colby, T.D. / Bahnson, B.J. / Chin, J.K. / Klinman, J.P. / Goldstein, B.M. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Active site modifications in a double mutant of liver alcohol dehydrogenase: structural studies of two enzyme-ligand complexes. Authors: Colby, T.D. / Bahnson, B.J. / Chin, J.K. / Klinman, J.P. / Goldstein, B.M. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 Title: A Link between Protein Structure and Enzyme Catalyzed Hydrogen Tunneling Authors: Bahnson, B.J. / Colby, T.D. / Chin, J.K. / Goldstein, B.M. / Klinman, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a71.cif.gz | 154.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a71.ent.gz | 121.4 KB | Display | PDB format |
PDBx/mmJSON format | 1a71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a71_validation.pdf.gz | 922.6 KB | Display | wwPDB validaton report |
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Full document | 1a71_full_validation.pdf.gz | 932.3 KB | Display | |
Data in XML | 1a71_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 1a71_validation.cif.gz | 41.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/1a71 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/1a71 | HTTPS FTP |
-Related structure data
Related structure data | 1a72C 2ohxS 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: 39864.258 Da / Num. of mol.: 2 / Mutation: F93W, V203A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Cellular location: CYTOPLASM / Gene: LADH F93W V203A / Organ: LIVER / Plasmid: PHAGEMID PBPP-LADH / Cellular location (production host): CYTOPLASM / Gene (production host): LADH F93W,V203A / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P00327, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: 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: 2.3 Å3/Da / Density % sol: 47.99 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.4 Details: 4MICROLITER HANGING DROPS TRIS PH 8.4 AT 4C, 5MM TRIFLUROETHANOL, 4% PEG400 EQUILIBRATED AGAINST WELLS CONTAINING 5MM TFE AND 18%PEG 400, vapor diffusion - hanging drop | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: YALE MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 38046 / % possible obs: 77.1 % / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2 / % possible all: 42.3 |
Reflection | *PLUS Num. measured all: 77199 |
Reflection shell | *PLUS % possible obs: 42.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OHX Resolution: 2→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED Cross valid method: UP TO LAST CG MINIMIZATION THROUGHOUT UNTIL LAST CG REFINEMENT σ(F): 2
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Displacement parameters | Biso mean: 22.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.268 |