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Yorodumi- PDB-1bep: EFFECT OF UNNATURAL HEME SUBSTITUTION ON KINETICS OF ELECTRON TRA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bep | ||||||
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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 / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / 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. / 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. / 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 | 1bep.cif.gz | 77 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bep.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 1bep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bep_validation.pdf.gz | 476.8 KB | Display | wwPDB validaton report |
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Full document | 1bep_full_validation.pdf.gz | 486.4 KB | Display | |
Data in XML | 1bep_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1bep_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/1bep ftp://data.pdbj.org/pub/pdb/validation_reports/be/1bep | HTTPS FTP |
-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: 33226.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE NATURALLY OCCURRING PROTOHEME REPLACED BY CHLOROCRUOROHEME 2-CHO, 4CH=CH2 PORPHYRIN Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PUC18CCPMI / Production host: Escherichia coli (E. coli) / References: UniProt: P00431, cytochrome-c peroxidase |
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#2: Chemical | ChemComp-CCH / [ |
#3: Water | ChemComp-HOH / |
-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: 30% MPD; 50 MM POTASSIUM PHOSPHATE, PH 6.0 |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Detector: AREA DETECTOR / Date: Jun 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: 22700 / % possible obs: 95 % / Observed criterion σ(I): 2 / Rsym value: 0.07836 |
Reflection shell | Highest resolution: 2.2 Å / Mean I/σ(I) obs: 2.77 / Rsym value: 0.227 |
-Processing
Software | Name: TNT / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→20 Å / Isotropic thermal model: TNT BCORREL / Stereochemistry target values: TNT PROTGEO /
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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