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Yorodumi- PDB-7d5w: Bovine heart cytochrome c oxidase in a catalytic intermediate of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d5w | ||||||||||||
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Title | Bovine heart cytochrome c oxidase in a catalytic intermediate of O at 1.84 angstrom resolution | ||||||||||||
Components | (Cytochrome c oxidase subunit ...) x 13 | ||||||||||||
Keywords | OXIDOREDUCTASE / cytochrome c oxidase membrane protein heme protein | ||||||||||||
Function / homology | Function and homology information TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / respiratory chain complex IV / Respiratory electron transport / regulation of oxidative phosphorylation / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase ...TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / respiratory chain complex IV / Respiratory electron transport / regulation of oxidative phosphorylation / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||||||||
Authors | Tsukihara, T. / Shimada, A. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Critical roles of the Cu B site in efficient proton pumping as revealed by crystal structures of mammalian cytochrome c oxidase catalytic intermediates. Authors: Shimada, A. / Hara, F. / Shinzawa-Itoh, K. / Kanehisa, N. / Yamashita, E. / Muramoto, K. / Tsukihara, T. / Yoshikawa, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d5w.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7d5w.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 7d5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/7d5w ftp://data.pdbj.org/pub/pdb/validation_reports/d5/7d5w | HTTPS FTP |
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-Related structure data
Related structure data | 7cp5C 7d5xC 5b1aS S: Starting model for refinement C: citing same article (ref.) |
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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
-Cytochrome c oxidase subunit ... , 13 types, 26 molecules ANBOCPDQERFSGTHUIVJWKXLYMZ
#1: Protein | Mass: 57093.852 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: 26068.404 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: 29725.328 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: 16913.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00423 #5: Protein | Mass: 12083.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00426 #6: Protein | Mass: 10233.528 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00428 #7: Protein | Mass: 9452.687 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07471 #8: Protein | Mass: 9411.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00429 #9: Protein | Mass: 8537.019 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P04038 #10: Protein | Mass: 6553.546 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07470 #11: Protein/peptide | Mass: 5442.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13183 #12: Protein/peptide | Mass: 5362.319 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00430 #13: Protein/peptide | Mass: 4738.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P10175 |
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-Sugars , 1 types, 23 molecules
#23: Sugar | ChemComp-DMU / |
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-Non-polymers , 16 types, 3126 molecules
#14: Chemical | ChemComp-HEA / #15: Chemical | #16: Chemical | #17: Chemical | ChemComp-NA / #18: Chemical | ChemComp-TGL / #19: Chemical | ChemComp-PGV / ( #20: Chemical | #21: Chemical | #22: Chemical | ChemComp-EDO / #24: Chemical | #25: Chemical | ChemComp-CHD / #26: Chemical | ChemComp-PEK / ( #27: Chemical | ChemComp-CDL / #28: Chemical | #29: Chemical | #30: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 4.04 Å3/Da / Density % sol: 69.6 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 6.7 / Details: PEG 4000, SODIUM PHOSPHATE BUFFER |
-Data collection
Diffraction | Mean temperature: 50 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→137 Å / Num. obs: 561788 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.033 / Net I/σ(I): 31.7 |
Reflection shell | Resolution: 1.84→1.86 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 13951 / Rpim(I) all: 0.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B1A Resolution: 1.84→39.915 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→39.915 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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