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Yorodumi- PDB-5ccp: HISTIDINE 52 IS A CRITICAL RESIDUE FOR RAPID FORMATION OF CYTOCHR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ccp | ||||||
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Title | HISTIDINE 52 IS A CRITICAL RESIDUE FOR RAPID FORMATION OF CYTOCHROME C PEROXIDASE COMPOUND I | ||||||
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 | Brown, K. / Shaw, A. / Miller, M.A. / Kraut, J. | ||||||
Citation | Journal: Biochemistry / Year: 1993 Title: Histidine 52 is a critical residue for rapid formation of cytochrome c peroxidase compound I. Authors: Erman, J.E. / Vitello, L.B. / Miller, M.A. / Shaw, A. / Brown, K.A. / Kraut, J. #1: Journal: J.Am.Chem.Soc. / Year: 1992 Title: Active-Site Mutations in Cytochrome C Peroxidase: A Critical Role for Histidine-52 in the Rate of Formation of Compound I Authors: Erman, J.E. / Vitello, L.B. / Miller, M.A. / Kraut, J. #2: Journal: Biochemistry / Year: 1991 Title: Conformational Change and Histidine Control of Heme Chemistry in Cytochrome C Peroxidase: Resonance Raman Evidence from Leu-52 and Gly-181 Mutants of C Peroxidase Authors: Smulevich, G. / Miller, M.A. / Kraut, J. / Spiro, T.G. #3: 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. #4: 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 | 5ccp.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ccp.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ccp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ccp_validation.pdf.gz | 474.6 KB | Display | wwPDB validaton report |
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Full document | 5ccp_full_validation.pdf.gz | 486.5 KB | Display | |
Data in XML | 5ccp_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 5ccp_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/5ccp ftp://data.pdbj.org/pub/pdb/validation_reports/cc/5ccp | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar 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: 33744.621 Da / Num. of mol.: 1 / Mutation: H52L 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 | 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: 2.6 Å3/Da / Density % sol: 52.74 % |
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Crystal grow | *PLUS pH: 6 / Method: microdialysis |
Components of the solutions | *PLUS Chemical formula: H2O |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. obs: 17653 / % possible obs: 95 % / Rmerge(I) obs: 0.052 |
-Processing
Software | Name: TNT / 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: 2.2 Å / Num. reflection obs: 17653 / Rfactor obs: 0.155 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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