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Yorodumi- PDB-1axe: CRYSTAL STRUCTURE OF THE ACTIVE-SITE MUTANT PHE93->TRP OF HORSE L... -
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-Basic information
Entry | Database: PDB / ID: 1axe | ||||||
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Title | CRYSTAL STRUCTURE OF THE ACTIVE-SITE MUTANT PHE93->TRP OF HORSE LIVER ALCOHOL DEHYDROGENASE IN COMPLEX WITH NAD AND INHIBITOR TRIFLUOROETHANOL | ||||||
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 / retinoic acid metabolic process / retinol 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. / Chin, J.K. / Goldstein, B.M. | ||||||
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.Biol.Chem. / Year: 1979 Title: Structural Differences between Apo-and Holoenzyme of Horse Liver Alcohol Dehydrogenase Authors: Eklund, H. / Branden, C.I. #11: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1axe.cif.gz | 150.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1axe.ent.gz | 122 KB | Display | PDB format |
PDBx/mmJSON format | 1axe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/1axe ftp://data.pdbj.org/pub/pdb/validation_reports/ax/1axe | HTTPS FTP |
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-Related structure data
Related structure data | 1axgC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.122993, 0.984919, 0.121686), Vector: |
-Components
#1: Protein | Mass: 39892.309 Da / Num. of mol.: 2 / Mutation: F93W Source method: isolated from a genetically manipulated source Details: HOLO-ENZYME / 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 | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 49.98 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: CRYSTALS WERE GROWN FROM HANGING DROPS. THE INITIAL DROP CONTAINING 16MG/ML PROTEIN, A 10X EXCESS OF NAD, 5MM TRIFLUOROETHANOL AND 5% V/V OF PEG400 IN 50MM TRIS-HCL PH 8.4 WERE EQUILIBRATED ...Details: CRYSTALS WERE GROWN FROM HANGING DROPS. THE INITIAL DROP CONTAINING 16MG/ML PROTEIN, A 10X EXCESS OF NAD, 5MM TRIFLUOROETHANOL AND 5% V/V OF PEG400 IN 50MM TRIS-HCL PH 8.4 WERE EQUILIBRATED AT 4 DEGREES C OVER WELLS OF SIMILAR COMPOSITION CONTAINING 15-17% PEG400., vapor diffusion - hanging drop, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 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: Sep 17, 1995 / Details: MONOCHROMATOR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→99 Å / Num. obs: 43756 / % possible obs: 85.2 % / Observed criterion σ(I): 2 / Redundancy: 1.83 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.31 / % possible all: 64.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OHX Resolution: 2→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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