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Yorodumi- PDB-2cyp: Crystal structure of yeast cytochrome C peroxidase refined at 1.7... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cyp | |||||||||
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Title | Crystal structure of yeast cytochrome C peroxidase refined at 1.7-angstroms resolution | |||||||||
Components | CYTOCHROME C PEROXIDASE | |||||||||
Keywords | OXIDOREDUCTASE (H2O2(A)) | |||||||||
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: 1.7 Å | |||||||||
Authors | Finzel, B.C. / Poulos, T.L. / Kraut, J. | |||||||||
Citation | 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. #1: Journal: Pept.Protein Rev. / Year: 1984 Title: Heme Enzyme Structure and Function Authors: Poulos, T.L. / Finzel, B.C. #2: Journal: J.Biol.Chem. / Year: 1980 Title: A Hypothetical Model of the Cytochrome C Peroxidase-Cytochrome C Electron Transfer Complex Authors: Poulos, T.L. / Kraut, J. #3: Journal: J.Biol.Chem. / Year: 1980 Title: The Stereochemistry of Peroxidase Catalysis Authors: Poulos, T.L. / Kraut, J. #4: Journal: J.Biol.Chem. / Year: 1980 Title: The Crystal Structure of Cytochrome C Peroxidase Authors: Poulos, T.L. / Freer, S.T. / Alden, R.A. / Edwards, S.L. / Skogland, U. / Takio, K. / Eriksson, B. / Xuong, N.-H. / Yonetani, T. / Kraut, J. #5: Journal: J.Biol.Chem. / Year: 1978 Title: Crystallographic Determination of the Heme Orientation and Location of the Cyanide Binding Site in Yeast Cytochrome C Peroxidase Authors: Poulos, T.L. / Freer, S.T. / Alden, R.A. / Xuong, N.H. / Edwards, S.L. / Hamlin, R.C. / Kraut, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cyp.cif.gz | 79.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cyp.ent.gz | 58.4 KB | Display | PDB format |
PDBx/mmJSON format | 2cyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/2cyp ftp://data.pdbj.org/pub/pdb/validation_reports/cy/2cyp | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: THIS ATOM WAS DESIGNATED HOH 595 BY THE DEPOSITORS. / 2: SEE REMARK 4. |
-Components
#1: Protein | Mass: 33571.238 Da / Num. of mol.: 1 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: Chemical | ChemComp-O / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.02 % | |||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.7 Å / Num. obs: 44888 / Num. measured all: 181721 / Rmerge(I) obs: 0.07 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor Rwork: 0.202 / Highest resolution: 1.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.7 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 44888 / Rfactor obs: 0.202 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: o_bond_d / Dev ideal target: 0.03 |