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Yorodumi- PDB-2pcc: CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pcc | ||||||
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Title | CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS, CYTOCHROME C PEROXIDASE AND CYTOCHROME C | ||||||
Components |
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Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / OXIDOREDUCTASE-ELECTRON TRANSPORT complex | ||||||
Function / homology | Function and homology information Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / peroxidase activity ...Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Pelletier, H. / Kraut, J. | ||||||
Citation | Journal: Science / Year: 1992 Title: Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c. Authors: Pelletier, 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. / Mauro, J.M. / Edwards, S.L. / Oatley, S.J. / Fishel, L.A. / Ashford, V.A. / Xuong, N.-H. / Kraut, J. #2: Journal: J.Mol.Biol. / Year: 1990 Title: High-Resolution Refinement of Yeast Iso-1-Cytochrome C and Comparisons with Other Eukaryotic Cytochromes C Authors: Louie, G.V. / Brayer, G.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pcc.cif.gz | 188.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pcc.ent.gz | 148.8 KB | Display | PDB format |
PDBx/mmJSON format | 2pcc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/2pcc ftp://data.pdbj.org/pub/pdb/validation_reports/pc/2pcc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | CHAINS LABELED A (CCP NUMBER 1) AND B (CYTOCHROME C NUMBER 1) REPRESENT ONE COMPLEX MOLECULE IN THE ASYMMETRIC UNIT, AND, LIKEWISE, CHAINS LABELED C (CCP NUMBER 2) AND D (CYTOCHROME C NUMBER 2) REPRESENT THE SECOND COMPLEX MOLECULE IN THE ASYMMETRIC UNIT. WATER MOLECULES NUMBERED 301 TO 554 ARE ASSOCIATED WITH THE FIRST COMPLEX, AND WATER MOLECULES NUMBERED 600 TO 848 ARE ASSOCIATED WITH THE SECOND COMPLEX. |
-Components
#1: Protein | Mass: 33769.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P00431 #2: Protein | Mass: 12073.835 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P00044 #3: Chemical | #4: Chemical | ChemComp-HEM / #5: Water | ChemComp-HOH / | Sequence details | IN ACCORDANCE WITH THE SEQUENCE NUMBERING FOR EUKARYOTIC CYTOCHROMES C, THE SEQUENCE NUMBERING FOR ...IN ACCORDANCE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.69 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.3 Å / Num. obs: 37845 / % possible obs: 93 % / Rmerge(I) obs: 0.044 |
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-Processing
Software |
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Refinement | Resolution: 2.3→6 Å / Rfactor Rwork: 0.167 Details: THE YEAST CCP USED HERE IS A RECOMBINANT [CALLED CCP(MI) AND EXPRESSED IN E. COLI] WHICH HAS A MET-ILE DIPEPTIDE FUSED TO THE N-TERMINUS. THIS MET-ILE DIPEPTIDE WAS NOT INCLUDED IN THIS ...Details: THE YEAST CCP USED HERE IS A RECOMBINANT [CALLED CCP(MI) AND EXPRESSED IN E. COLI] WHICH HAS A MET-ILE DIPEPTIDE FUSED TO THE N-TERMINUS. THIS MET-ILE DIPEPTIDE WAS NOT INCLUDED IN THIS STRUCTURE DUE TO DISORDER. THERE WAS UNEXPLAINED ELECTRON DENSITY ABOVE THE HEME IRON INTO WHICH WATER MOLECULES ALONE COULD NOT BE MODELED. AN SO- GROUP, A POSSIBLE DEGRADATION PRODUCT OF DTT, WAS PLACED HERE AND WAS TREATED AS AN INCOMPLETE SULFATE ION DURING REFINEMENT. THIS IS NOT A SULFATE ION. IT IS ONLY CALLED A SULFATE ION FOR SIMPLICITY. | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→6 Å
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Refinement | *PLUS Highest resolution: 2.3 Å / Rfactor obs: 0.172 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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