[English] 日本語
Yorodumi- PDB-2oxi: REFINED CRYSTAL STRUCTURE OF CU-SUBSTITUTED ALCOHOL DEHYDROGENASE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oxi | ||||||
---|---|---|---|---|---|---|---|
Title | REFINED CRYSTAL STRUCTURE OF CU-SUBSTITUTED ALCOHOL DEHYDROGENASE AT 2.1 ANGSTROMS RESOLUTION | ||||||
Components | ALCOHOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE(NAD(A)-CHOH(D)) | ||||||
Function / homology | Function and homology information alcohol dehydrogenase activity, zinc-dependent / ethanol oxidation / NAD-retinol dehydrogenase 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 / Resolution: 2.1 Å | ||||||
Authors | Al-Karadaghi, S. / Cedergren-Zeppezauer, E.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Refined structure of Cu-substituted alcohol dehydrogenase at 2.1 A resolution. Authors: Al-Karadaghi, S. / Cedergren-Zeppezauer, E.S. / Dauter, Z. / Wilson, K.S. #1: Journal: FEBS Lett. / Year: 1992 Title: Copper(II)-Substituted Horse Liver Alcohol Dehydrogenase: Structure of the Minor Species Authors: Formicka, G. / Zeppezauer, M. / Fey, F. / Huettermann, J. #2: Journal: Biochim.Biophys.Acta / Year: 1987 Title: Electronic Absorption and Epr Spectroscopy of Copper Alcohol Dehydrogenase: Pink, Violet and Green Forms of a Type 1 Copper Center Analog Authors: Maret, W. / Kozlowski, H. #3: Journal: J.Am.Chem.Soc. / Year: 1986 Title: Resonance Raman Spectroscopy of Blue Copper Proteins: Ligand and Coenzyme Effects in Copper(II)-Substituted Liver Alcohol Dehydrogenase Authors: Maret, W. / Shiemke, A.K. / Wheeler, W.D. / Loehr, T.M. / Sanders-Loehr, J. #4: Journal: Biochemistry / Year: 1983 Title: Resonance Raman Spectra of Copper(II)-Substituted Liver Alcohol Dehydrogenase: A Type 1 Copper Analogue Authors: Maret, W. / Zeppezauer, M. / Sanders-Loehr, J. / Loehr, T.M. #5: Journal: Biochim.Biophys.Acta / Year: 1983 Title: An Epr Study of the Blue Copper Center in Horse Liver Alcohol Dehydrogenase Authors: Maret, W. / Zeppezauer, M. / Desideri, A. / Morpurgo, L. / Rotilio, G. #6: Journal: FEBS Lett. / Year: 1981 Title: Ligand Binding to the Blue Copper Center of Horse Liver Alcohol Dehydrogenase Authors: Maret, W. / Zeppezauer, M. / Desideri, A. / Morpurgo, L. / Rotilio, G. #7: Journal: J.Inorg.Biochem. / Year: 1980 Title: Active Site-Specific Reconstituted Copper(II) Horse Liver Alcohol Dehydrogenase: A Biological Model for Type 1 Cu and its Changes Upon Ligand Binding and Conformational Transitions Authors: Maret, W. / Dietrich, H. / Ruf, H.-H. / Zeppezauer, M. | ||||||
History |
| ||||||
Remark 650 | HELIX RESIDUES GLY 181 - VAL 189 OF HELICES *HAA* AND *HAB* FORM A PI-HELIX (CLASS 3, 1.5 TURNS). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2oxi.cif.gz | 164.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2oxi.ent.gz | 129.1 KB | Display | PDB format |
PDBx/mmJSON format | 2oxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/2oxi ftp://data.pdbj.org/pub/pdb/validation_reports/ox/2oxi | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: CIS PROLINE - PRO A 62 / 2: CIS PROLINE - PRO B 62 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.49169, 0.12942, -0.86109), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. CORRESP. EULERIAN ANGLES (THETA1, THETA2, THETA3) 274.5813 120.1650 264.8520 CORRESP. SPHERICAL POLAR ANGLES (PSI, PHI, KAPPA) 85.7848 30.0067 180.2826 CORRESP. ROTATION ANGLE 179.7174 ABOUT AXIS -0.8636 -0.0735 0.4987 | |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase |
---|
-Non-polymers , 5 types, 453 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.36 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Method: microdialysis | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 12 Å / Num. obs: 41119 / Num. measured all: 81533 / Rmerge(I) obs: 0.044 |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Rfactor Rwork: 0.16 / Rfactor obs: 0.16 / Highest resolution: 2.1 Å Details: THERE IS DISCRETE DISORDER IN RESIDUES CYS A 46 CYS A 281 CYS A 282 CYS B 46 CYS B 282 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.1 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 12 Å / Num. reflection obs: 41119 / Rfactor obs: 0.161 / Rfactor Rwork: 0.161 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|