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- PDB-6jy4: Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jy4 | |||||||||||||||||||||
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Title | Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Reduced State | |||||||||||||||||||||
![]() | (Cytochrome c oxidase subunit ...) x 13 | |||||||||||||||||||||
![]() | OXIDOREDUCTASE / Monomer / Fully Reduced | |||||||||||||||||||||
Function / homology | ![]() TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / : ...TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / : / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Mitochondrial protein degradation / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / central nervous system development / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Shinzawa-Itoh, K. / Muramoto, K. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Monomeric structure of an active form of bovine cytochromecoxidase. Authors: Shinzawa-Itoh, K. / Sugimura, T. / Misaki, T. / Tadehara, Y. / Yamamoto, S. / Hanada, M. / Yano, N. / Nakagawa, T. / Uene, S. / Yamada, T. / Aoyama, H. / Yamashita, E. / Tsukihara, T. / ...Authors: Shinzawa-Itoh, K. / Sugimura, T. / Misaki, T. / Tadehara, Y. / Yamamoto, S. / Hanada, M. / Yano, N. / Nakagawa, T. / Uene, S. / Yamada, T. / Aoyama, H. / Yamashita, E. / Tsukihara, T. / Yoshikawa, S. / Muramoto, K. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 785.7 KB | Display | ![]() |
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PDB format | ![]() | 638.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.5 MB | Display | ![]() |
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Full document | ![]() | 3.6 MB | Display | |
Data in XML | ![]() | 76 KB | Display | |
Data in CIF | ![]() | 102.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jy3C ![]() 5b1bS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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, 13 molecules ABCDEFGHIJKLM
#1: Protein | Mass: 57093.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 26068.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 29957.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 17179.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 12453.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 10684.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 9549.802 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 10039.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 8494.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 6682.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 6365.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein/peptide | Mass: 5449.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein/peptide | Mass: 4967.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 12 types, 630 molecules ![](data/chem/img/HEA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CQX.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CQX.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/HOH.gif)
#14: Chemical | #15: Chemical | ChemComp-CU / | #16: Chemical | ChemComp-MG / | #17: Chemical | #18: Chemical | ChemComp-CQX / ( #19: Chemical | #20: Chemical | #21: Chemical | ChemComp-CUA / | #22: Chemical | ChemComp-CHD / | #23: Chemical | ChemComp-ZN / | #24: Chemical | ChemComp-PEK / ( | #25: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.04 Å3/Da / Density % sol: 75.6 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / Details: sodium phosphate, PEG 4000, DM |
-Data collection
Diffraction | Mean temperature: 50 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 27, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→200 Å / Num. obs: 278336 / % possible obs: 89.5 % / Redundancy: 9 % / Rpim(I) all: 0.032 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.9→1.92 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 9391 / CC1/2: 0.734 / Rpim(I) all: 0.373 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5B1B Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.391 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.214 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→40 Å
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Refine LS restraints |
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