[English] 日本語
Yorodumi- PDB-2pcb: CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pcb | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS, CYTOCHROME C PEROXIDASE AND CYTOCHROME C | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / OXIDOREDUCTASE-ELECTRON TRANSPORT complex | ||||||
Function / homology | Function and homology information cytochrome c-heme linkage / cytochrome complex / cytochrome-c peroxidase / positive regulation of cysteine-type endopeptidase activity / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / response to reactive oxygen species ...cytochrome c-heme linkage / cytochrome complex / cytochrome-c peroxidase / positive regulation of cysteine-type endopeptidase activity / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / positive regulation of apoptotic process / lipid binding / heme binding / apoptotic process / mitochondrion / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 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 Three Dimensional Structure of Horse Heart Cytochrome C Authors: Bushnell, G.W. / Louie, G.V. / Brayer, G.D. #3: Journal: J.Biol.Chem. / Year: 1987 Title: Co-Crystals of Yeast Cytochrome C Peroxidase and Horse Heart Cytochrome C Authors: Poulos, T.L. / Sheriff, S. / Howard, A.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2pcb.cif.gz | 162 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2pcb.ent.gz | 127.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pcb_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2pcb_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2pcb_validation.xml.gz | 43.2 KB | Display | |
Data in CIF | 2pcb_validation.cif.gz | 58.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/2pcb ftp://data.pdbj.org/pub/pdb/validation_reports/pc/2pcb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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) Organ: HEART / References: UniProt: P00431 #2: Protein | | Mass: 11725.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Organ: HEART / References: UniProt: P00004 #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.2 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 24671 / % possible obs: 93 % / Rmerge(I) obs: 0.055 |
---|
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.8→6 Å / Rfactor Rwork: 0.178 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. AFTER FINAL REFINEMENT THERE WAS ADDITIONAL ELECTRON DENSITY FOUND IN THE ASYMMETRIC UNIT WHICH HAS BEEN ATTRIBUTED TO A PARTIALLY OCCUPIED SECOND CYTOCHROME C MOLECULE. THE COORDINATES FOR A POSSIBLE SECOND CYTOCHROME C SITE HAVE NOT BEEN INCLUDED IN THIS ENTRY. SEE REFERENCE 1 FOR DETAILS. | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→6 Å
| ||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Rfactor obs: 0.178 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
|