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Yorodumi- PDB-1bek: EFFECT OF UNNATURAL HEME SUBSTITUTION ON KINETICS OF ELECTRON TRA... -
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-Basic information
Entry | Database: PDB / ID: 1bek | ||||||
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Title | EFFECT OF UNNATURAL HEME SUBSTITUTION ON KINETICS OF ELECTRON TRANSFER IN CYTOCHROME C PEROXIDASE | ||||||
Components | YEAST CYTOCHROME C PEROXIDASE | ||||||
Keywords | PEROXIDASE / OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information cytochrome-c peroxidase / cytochrome-c peroxidase activity / peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Miller, M.A. / Kraut, J. | ||||||
Citation | Journal: To be Published Title: Effect of Unnatural Heme Substitution on Kinetics of Electron Transfer in Cytochrome C Peroxidase Authors: Miller, M.A. / Millett, F. / Durham, B. / Kraut, J. / Mei, H.K. / Ashford, V.A. / Xuong, N.-H. / Kraut, J. #1: Journal: Biochemistry / Year: 1990 Title: X-Ray Structures of Recombinant Yeast Cytochrome C Peroxidase and Three Heme-Cleft Mutants Prepared by Site-Directed Mutagenesis Authors: Wang, J.M. / Mauro, M. / Edwards, S.L. / Oatley, S.J. / Fishel, L.A. / Ashford, V.A. / Xuong, N.H. / Kraut, J. #2: Journal: J.Biol.Chem. / Year: 1984 Title: Crystal Structure of Yeast Cytochrome C Peroxidase Refined at 1.7-A Resolution Authors: Finzel, B.C. / Poulos, T.L. / Kraut, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bek.cif.gz | 77.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bek.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 1bek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/1bek ftp://data.pdbj.org/pub/pdb/validation_reports/be/1bek | HTTPS FTP |
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-Related 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: 33134.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE NATURALLY OCCURRING PROTOHEME REPLACED BY MESOHEME (2,4-CH2-CH3 PORPHYRIN) Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P00431, cytochrome-c peroxidase |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
Compound details | THIS ENZYME WAS PURIFIED IN THE APO FORM, THEN RECONSTITUTED WITH THE UNNATURAL MESOHEME PROSTHETIC ...THIS ENZYME WAS PURIFIED IN THE APO FORM, THEN RECONSTITU |
Sequence details | THIS CYTOCHROME C PEROXIDASE DIFFERS FROM THE PREVIOUSLY DEPOSITED STRUCTURE (PROTEIN DATA BANK ...THIS CYTOCHROME |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54 % |
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Crystal grow | pH: 6 / Details: 50 MM POTASSIUM PHOSPHATE; 30% MPD, pH 6 |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: May 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.2 Å / Num. obs: 17694 / % possible obs: 95 % / Observed criterion σ(I): 2 / Rsym value: 0.08421 |
Reflection shell | Highest resolution: 2.2 Å / Mean I/σ(I) obs: 2.15 / Rsym value: 0.17 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→20 Å Details: THE SOLUTION WAS OBTAINED USING A>B>C AS THE UNIT CELL PARAMETERS. COORDINATES FOR RESIDUES -1, 0 AND 1 ARE NOT INCLUDED IN THIS ENTRY BECAUSE THESE RESIDUES COULD NOT BE RESOLVED IN THE ...Details: THE SOLUTION WAS OBTAINED USING A>B>C AS THE UNIT CELL PARAMETERS. COORDINATES FOR RESIDUES -1, 0 AND 1 ARE NOT INCLUDED IN THIS ENTRY BECAUSE THESE RESIDUES COULD NOT BE RESOLVED IN THE FINAL ELECTRON DENSITY MAPS. ALTHOUGH COORDINATES FOR RESIDUE 2 ARE INCLUDED, THEY ARE NOT WELL DEFINED DUE TO VERY LARGE TEMPERATURE FACTORS (OVER 100 ANGSTROMS SQUARED).
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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