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Yorodumi- PDB-1axg: CRYSTAL STRUCTURE OF THE VAL203->ALA MUTANT OF LIVER ALCOHOL DEHY... -
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-Basic information
Entry | Database: PDB / ID: 1axg | ||||||
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Title | CRYSTAL STRUCTURE OF THE VAL203->ALA MUTANT OF LIVER ALCOHOL DEHYDROGENASE COMPLEXED WITH COFACTOR NAD AND INHIBITOR TRIFLUOROETHANOL SOLVED TO 2.5 ANGSTROM RESOLUTION | ||||||
Components | ALCOHOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / OXIDOREDUCTASE (NAD(A)-CHOH(D)) / ALCOHOL DEHYDROGENASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Colby, T.D. / Chin, J.K. / Bahnson, B.J. / Goldstein, B.M. / Klinman, J.P. | ||||||
Citation | 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. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 A Resolution Authors: Al-Karadaghi, S. / Cedergren-Zeppezauer, E.S. / Hovmoller, S. / Petratos, K. / Terry, H. / Wilson, K.S. #2: Journal: J.Biol.Chem. / Year: 1986 Title: Interdomain Motion in Liver Alcohol Dehydrogenase. Structural and Energetic Analysis of the Hinge Bending Mode Authors: Colonna-Cesari, F. / Perahia, D. / Karplus, M. / Eklund, H. / Branden, C.I. / Tapia, O. #3: Journal: Biochemistry / Year: 1984 Title: Crystallographic Investigations of Nicotinamide Adenine Dinucleotide Binding to Horse Liver Alcohol Dehydrogenase Authors: Eklund, H. / Samama, J.P. / Jones, T.A. #4: Journal: Biochemistry / Year: 1983 Title: Crystal-Structure Determination of Reduced Nicotinamide Adenine Dinucleotide Complex with Horse Liver Alcohol Dehydrogenase Maintained in its Apo Conformation by Zinc-Bound Imidazole Authors: Cedergren-Zeppezauer, E. #5: Journal: J.Biol.Chem. / Year: 1983 Title: Three-Dimensional Structure of Isonicotinimidylated Liver Alcohol Dehydrogenase Authors: Plapp, B.V. / Eklund, H. / Jones, T.A. / Branden, C.I. #6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983 Title: Crystal Structures of the Active Site in Specifically Metal-Depleted and Cobalt-Substituted Horse Liver Alcohol Dehydrogenase Derivatives Authors: Schneider, G. / Eklund, H. / Cedergren-Zeppezauer, E. / Zeppezauer, M. #7: Journal: Biochemistry / Year: 1982 Title: Pyrazole Binding in Crystalline Binary and Ternary Complexes with Liver Alcohol Dehydrogenase Authors: Eklund, H. / Samama, J.P. / Wallen, L. #8: Journal: Biochemistry / Year: 1982 Title: Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogenase. Binding of 1,4,5,6-Tetrahydronicotinamide Adenine Dinucleotide and Trans-4-(N,N- ...Title: Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogenase. Binding of 1,4,5,6-Tetrahydronicotinamide Adenine Dinucleotide and Trans-4-(N,N-Dimethylamino)Cinnamaldehyde to the Enzyme Authors: Cedergren-Zeppezauer, E. / Samama, J.P. / Eklund, H. #9: 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. #10: Journal: J.Mol.Biol. / Year: 1981 Title: Structure of a Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 A Resolution Authors: Eklund, H. / Samama, J.P. / Wallen, L. / Branden, C.I. / Akeson, A. / Jones, T.A. #11: Journal: Eur.J.Biochem. / Year: 1981 Title: 5-Methylnicotinamide-Adenine Dinucleotide. Kinetic Investigation with Major and Minor Isoenzymes of Liver Alcohol Dehydrogenase and Structural Determination of its Binary Complex with Alcohol Dehydrogenase Authors: Samama, J.P. / Wrixon, A.D. / Biellmann, J.F. #12: Journal: Eur.J.Biochem. / Year: 1979 Title: X-Ray Studies of the Binding of Cibacron Blue F3Ga to Liver Alcohol Dehydrogenase Authors: Biellmann, J.F. / Samama, J.P. / Branden, C.I. / Eklund, H. #13: Journal: J.Biol.Chem. / Year: 1979 Title: Structural Differences between Apo-and Holoenzyme of Horse Liver Alcohol Dehydrogenase Authors: Eklund, H. / Branden, C.I. #14: Journal: J.Biol.Chem. / Year: 1978 Title: Subunit Conformation of Yeast Alcohol Dehydrogenase Authors: Jornvall, H. / Eklund, H. / Branden, C.I. #15: Journal: J.Mol.Biol. / Year: 1978 Title: Crystallization of Liver Alcohol Dehydrogenase Activated by the Modification of Amino Groups Authors: Plapp, B.V. / Zeppezauer, E. / Branden, C.I. #16: Journal: J.Mol.Biol. / Year: 1978 Title: Crystallography of Liver Alcohol Dehydrogenase Complexed with Substrates Authors: Plapp, B.V. / Eklund, H. / Branden, C.I. #17: Journal: Eur.J.Biochem. / Year: 1977 Title: X-Ray Investigation of the Binding of 1,10-Phenanthroline and Imidazole to Horse-Liver Alcohol Dehydrogenase Authors: Boiwe, T. / Branden, C.I. #18: Journal: Eur.J.Biochem. / Year: 1977 Title: The Crystal Structure of Complexes between Horse Liver Alcohol Dehydrogenase and the Coenzyme Analogues 3-Iodopyridine-Adenine Dinucleotide and Pyridine-Adenine Dinucleotide Authors: Samama, J.P. / Zeppezauer, E. / Biellmann, J.F. / Branden, C.I. #19: Journal: J.Mol.Biol. / Year: 1976 Title: Structural Comparisons of Mammalian, Yeast and Bacillar Alcohol Dehydrogenases Authors: Eklund, H. / Branden, C.I. / Jornvall, H. #20: Journal: J.Mol.Biol. / Year: 1976 Title: Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 A Resolution Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A. #21: Journal: STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN Year: 1975 Title: The Binding of Nucleotides to Horse Liver Alcohol Authors: Nordstrom, B. / Branden, C.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1axg.cif.gz | 286.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1axg.ent.gz | 236.9 KB | Display | PDB format |
PDBx/mmJSON format | 1axg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1axg_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 1axg_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 1axg_validation.xml.gz | 58.2 KB | Display | |
Data in CIF | 1axg_validation.cif.gz | 79.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/1axg ftp://data.pdbj.org/pub/pdb/validation_reports/ax/1axg | HTTPS FTP |
-Related structure data
Related structure data | 1axeC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 39825.223 Da / Num. of mol.: 4 / Mutation: V203A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Cellular location: CYTOPLASM / Gene: LADH CDNA / Organ: LIVER / Plasmid: PBPP-LADH / Cellular location (production host): CYTOPLASM / Gene (production host): LADH CDNA / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P00327, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-ETF / #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: 2.04 Å3/Da / Density % sol: 39.76 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.4 / Details: pH 8.4 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 39 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 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: Dec 11, 1995 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 40627 / % possible obs: 93.1 % / Redundancy: 2.43 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 2.38 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.273 / % possible all: 86.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OHX Resolution: 2.5→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Xplor file |
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