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Yorodumi- PDB-5b1a: Bovine heart cytochrome c oxidase in the fully oxidized state at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b1a | ||||||||||||
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Title | Bovine heart cytochrome c oxidase in the fully oxidized state at 1.5 angstrom resolution | ||||||||||||
Components | (Cytochrome c oxidase subunit ...) x 13 | ||||||||||||
Keywords | OXIDOREDUCTASE / Proton pump / Heme / Respiratory chain | ||||||||||||
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: 1.5 Å | ||||||||||||
Authors | Yano, N. / Muramoto, K. / Shimada, A. / Takemura, S. / Baba, J. / Fujisawa, H. / Mochizuki, M. / Shinzawa-Itoh, K. / Yamashita, E. / Tsukihara, T. / Yoshikawa, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2016 Title: The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle. Authors: Yano, N. / Muramoto, K. / Shimada, A. / Takemura, S. / Baba, J. / Fujisawa, H. / Mochizuki, M. / Shinzawa-Itoh, K. / Yamashita, E. / 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 | 5b1a.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5b1a.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 5b1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/5b1a ftp://data.pdbj.org/pub/pdb/validation_reports/b1/5b1a | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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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 #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 #4: Protein | Mass: 17179.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00423 #5: Protein | Mass: 12453.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00426 #6: Protein | Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00428 #7: Protein | Mass: 9629.782 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07471 #8: Protein | Mass: 10039.244 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: 6682.726 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07470 #11: Protein | Mass: 6365.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13183 #12: Protein/peptide | Mass: 5449.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00430 #13: Protein/peptide | Mass: 4967.756 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, 4 molecules
#28: Sugar | ChemComp-DMU / |
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-Non-polymers , 15 types, 3651 molecules
#14: Chemical | ChemComp-HEA / #15: Chemical | #16: Chemical | #17: Chemical | #18: Chemical | #19: Chemical | ChemComp-PGV / ( #20: Chemical | ChemComp-TGL / #21: Chemical | #22: Chemical | ChemComp-CHD / #23: Chemical | #24: Chemical | #25: Chemical | ChemComp-CDL / #26: Chemical | ChemComp-PEK / ( #27: Chemical | #29: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.49 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 6.8 / Details: PEG 4000, Sodium phosphate |
-Data collection
Diffraction | Mean temperature: 50 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 23, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→200 Å / Num. obs: 1041861 / % possible obs: 100 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 1.5→1.52 Å / Redundancy: 14.8 % / Mean I/σ(I) obs: 3.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→40 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.201 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The authors state that the distance between O1 and O2 of peroxide was fixed at 1.55 angstrom during structure refinement.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.012 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→40 Å
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Refine LS restraints |
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