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Yorodumi- PDB-2y69: Bovine heart cytochrome c oxidase re-refined with molecular oxygen -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y69 | ||||||
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Title | Bovine heart cytochrome c oxidase re-refined with molecular oxygen | ||||||
Components |
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Keywords | ELECTRON TRANSPORT / COMPLEX IV / PROTON PUMPS / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / Cytoprotection by HMOX1 / respiratory chain complex IV / regulation of oxidative phosphorylation / Respiratory electron transport / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase ...TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / Cytoprotection by HMOX1 / respiratory chain complex IV / regulation of oxidative phosphorylation / Respiratory electron transport / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / cytochrome-c oxidase activity / ATP synthesis coupled electron transport / enzyme regulator activity / central nervous system development / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / nucleoplasm / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Kaila, V.R.I. / Oksanen, E. / Goldman, A. / Verkhovsky, M.I. / Sundholm, D. / Wikstrom, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: A Peroxide Bridge between Fe and Cu Ions in the O2 Reduction Site of Fully Oxidized Cytochrome C Oxidase Could Suppress the Proton Pump. Authors: Aoyama, H. / Muramoto, K. / Shinzawa-Itoh, K. / Hirata, K. / Yamashita, E. / Tsukihara, T. / Ogura, T. / Yoshikawa, S. | ||||||
History |
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Remark 0 | THIS ENTRY 2Y69 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R3ABMSF) ...THIS ENTRY 2Y69 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R3ABMSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 3ABM: H.AOYAMA,K.MURAMOTO,K.SHINZAWA-ITOH,K.HIRATA,E.YAMASHITA, T.TSUKIHARA,T.OGURA,S.YOSHIKAWA |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y69.cif.gz | 752 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y69.ent.gz | 630.4 KB | Display | PDB format |
PDBx/mmJSON format | 2y69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/2y69 ftp://data.pdbj.org/pub/pdb/validation_reports/y6/2y69 | HTTPS FTP |
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-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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2 |
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Unit cell |
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-Components
-CYTOCHROME C OXIDASE SUBUNIT ... , 8 types, 16 molecules ANBOCPDQERFSHULY
#1: Protein | Mass: 57065.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P00396, cytochrome-c oxidase #2: Protein | Mass: 26040.393 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P68530, cytochrome-c oxidase #3: Protein | Mass: 29957.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P00415, cytochrome-c oxidase #4: Protein | Mass: 19602.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P00423, cytochrome-c oxidase #5: Protein | Mass: 16758.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P00426, cytochrome-c oxidase #6: Protein | Mass: 13852.807 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P00428, cytochrome-c oxidase #8: Protein | Mass: 10170.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P00429, cytochrome-c oxidase #12: Protein | Mass: 7342.661 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P00430, cytochrome-c oxidase |
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-CYTOCHROME C OXIDASE POLYPEPTIDE ... , 5 types, 10 molecules GTIVJWKXMZ
#7: Protein | Mass: 10899.382 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P07471, cytochrome-c oxidase #9: Protein | Mass: 8626.179 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P04038, cytochrome-c oxidase #10: Protein | Mass: 9076.522 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P07470, cytochrome-c oxidase #11: Protein | Mass: 9077.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P13183, cytochrome-c oxidase #13: Protein | Mass: 7650.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P10175, cytochrome-c oxidase |
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-Sugars , 1 types, 2 molecules
#23: Sugar |
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-Non-polymers , 10 types, 1074 molecules
#14: Chemical | ChemComp-HEA / #15: Chemical | #16: Chemical | #17: Chemical | #18: Chemical | ChemComp-CHD / #19: Chemical | #20: Chemical | #21: Chemical | ChemComp-PGV / ( #22: Chemical | #24: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.17 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 3ABM |
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 0 Å2 |
-Processing
Software | Name: REFMAC / Version: 5.5.0066 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→64.15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.281 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R3ABMSF.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.538 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→64.15 Å
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