+Open data
-Basic information
Entry | Database: PDB / ID: 1mgo | ||||||
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Title | Horse Liver Alcohol Dehydrogenase Phe93Ala Mutant | ||||||
Components | Alcohol Dehydrogenase E chain | ||||||
Keywords | OXIDOREDUCTASE / Dehydrogenase / Alcohol / Nicotinamide Coenzyme / Mutant / Substrate binding site | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Rubach, J.K. / Plapp, B.V. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Mobility of Fluorobenzyl Alcohols Bound to Liver Alcohol Dehydrogenases as Determined by NMR and X-ray Crystallographic Studies Authors: Rubach, J.K. / Plapp, B.V. #1: Journal: Biochemistry / Year: 1994 Title: Structures of Horse Liver Alcohol Dehydrogenase Complexed with NAD+ and Substituted Benzyl Alcohols. Authors: Ramaswamy, S. / Eklund, H. / Plapp, B.V. #2: Journal: J.Biol.Chem. / Year: 1982 Title: Binding of Substrate in a Ternary Complex of Horse Liver Alcohol Dehydrogenase Authors: Eklund, H. / Plapp, B.V. / Samama, J.P. / Branden, C.I. #3: Journal: J.Mol.Biol. / Year: 1981 Title: Structure of a Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 Angstrom Resolution Authors: Eklund, H. / Samma, J.P. / Wallen, L. / Branden, C.I. / Akeson, A. / Jones, T.A. #4: Journal: J.Mol.Biol. / Year: 1976 Title: Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 Angstroms Resolution Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ONE ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ONE BIOLOGICALLY ACTIVE DIMERIC MOLECULE AB (2 CHAINS). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mgo.cif.gz | 293.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mgo.ent.gz | 235.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mgo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/1mgo ftp://data.pdbj.org/pub/pdb/validation_reports/mg/1mgo | HTTPS FTP |
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-Related structure data
Related structure data | 1mg0C 1hldS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39777.180 Da / Num. of mol.: 2 / Mutation: F93A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: M64864 / Plasmid: pBPP / Production host: Escherichia coli (E. coli) / Strain (production host): CJ236 / References: UniProt: P00327, alcohol dehydrogenase |
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-Non-polymers , 5 types, 474 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MPD / ( | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.18 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: dialysis / pH: 7 / Details: MPD, pH 7.0, Dialysis, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 253 ℃ / pH: 6.7 / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.2→20 Å / Num. obs: 199442 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.25 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 5.3 | ||||||||||||||||||
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 1.46 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.29 / % possible all: 84.5 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 86.6 % / Num. measured all: 455785 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 84.5 % / Rmerge(I) obs: 0.29 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HLD Resolution: 1.2→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.199 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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