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Yorodumi- PDB-7ccp: EFFECT OF ARGININE-48 REPLACEMENT ON THE REACTION BETWEEN CYTOCHR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ccp | ||||||
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Title | EFFECT OF ARGININE-48 REPLACEMENT ON THE REACTION BETWEEN CYTOCHROME C PEROXIDASE AND HYDROGEN PEROXIDE | ||||||
Components | CYTOCHROME C PEROXIDASE | ||||||
Keywords | 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 | Wang, J. / Miller, M.A. / Kraut, J. | ||||||
Citation | Journal: Biochemistry / Year: 1993 Title: Effect of arginine-48 replacement on the reaction between cytochrome c peroxidase and hydrogen peroxide. Authors: Vitello, L.B. / Erman, J.E. / Miller, M.A. / Wang, J. / 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. / Mauro, J.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 Angstroms 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 | 7ccp.cif.gz | 77.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ccp.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ccp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ccp_validation.pdf.gz | 474.2 KB | Display | wwPDB validaton report |
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Full document | 7ccp_full_validation.pdf.gz | 482.6 KB | Display | |
Data in XML | 7ccp_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 7ccp_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/7ccp ftp://data.pdbj.org/pub/pdb/validation_reports/cc/7ccp | 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: 33725.574 Da / Num. of mol.: 1 / Mutation: R48L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P00431, cytochrome-c peroxidase |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
Compound details | ACTIVE SITE WATER MOLECULE HOH-595 HAD VERY LOW OCCUPANCY IN THE R48L MUTANT, AND WAS NOT INCLUDED ...ACTIVE SITE WATER MOLECULE HOH-595 HAD VERY LOW OCCUPANCY IN THE R48L MUTANT, AND WAS NOT INCLUDED IN THE MODEL. |
Sequence details | THE SEQUENCE DIFFERS FROM THAT REPORTED FOR 2CYP AT RESIDUE 272. IN THE PRESENT ENTRY, THIS RESIDUE ...THE SEQUENCE DIFFERS FROM THAT REPORTED FOR 2CYP AT RESIDUE 272. IN THE PRESENT ENTRY, THIS RESIDUE IS REPORTED AS ASN. THIS CORRECTS AN ERROR INTRODUCED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.9 % | |||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 15996 / Rmerge(I) obs: 0.071 / Num. measured all: 126954 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 2.2 Å /
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Refinement step | Cycle: LAST / Highest resolution: 2.2 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Num. reflection obs: 15996 / Rfactor obs: 0.159 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |