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Yorodumi- PDB-2ccp: X-RAY STRUCTURES OF RECOMBINANT YEAST CYTOCHROME C PEROXIDASE AND... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ccp | ||||||
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Title | X-RAY STRUCTURES OF RECOMBINANT YEAST CYTOCHROME C PEROXIDASE AND THREE HEME-CLEFT MUTANTS PREPARED BY SITE-DIRECTED MUTAGENESIS | ||||||
Components | YEAST 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. / Mauro, J.M. / Edwards, S.L. / Oatley, S.J. / Fishel, L.A. / Ashford, V.A. / Xuong, N.-H. / Kraut, J. | ||||||
Citation | 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. #1: 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 | 2ccp.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ccp.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ccp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ccp_validation.pdf.gz | 476 KB | Display | wwPDB validaton report |
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Full document | 2ccp_full_validation.pdf.gz | 487.1 KB | Display | |
Data in XML | 2ccp_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 2ccp_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/2ccp ftp://data.pdbj.org/pub/pdb/validation_reports/cc/2ccp | 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: 33768.621 Da / Num. of mol.: 1 / Mutation: D235N 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 / |
Sequence details | RESIDUES ARE NUMBERED TO BE CONSISTENT WITH THE SEQUENCE OF THE NATIVE (2CYP) STRUCTURE. THUS THE ...RESIDUES ARE NUMBERED TO BE CONSISTENT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.5 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / 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 Num. obs: 16555 / Rmerge(I) obs: 0.0425 |
-Processing
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Refinement | Rfactor obs: 0.147 / Highest resolution: 2.2 Å Details: 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 ...Details: 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). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.2 Å
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Refine LS restraints |
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