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- PDB-8h8s: Bovine Heart Cytochrome c Oxidase in the Calcium-bound Fully Redu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8h8s | |||||||||||||||
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Title | Bovine Heart Cytochrome c Oxidase in the Calcium-bound Fully Reduced State | |||||||||||||||
![]() | (Cytochrome c oxidase subunit ...) x 13 | |||||||||||||||
![]() | OXIDOREDUCTASE / Calcium / 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 | ![]() ![]() ![]() | |||||||||||||||
![]() | Muramoto, K. / Shinzawa-Itoh, K. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Calcium-bound structure of bovine cytochrome c oxidase. Authors: Muramoto, K. / Shinzawa-Itoh, 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 | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 19.6 MB | Display | ![]() |
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Full document | ![]() | 20 MB | Display | |
Data in XML | ![]() | 177.1 KB | Display | |
Data in CIF | ![]() | 232.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h8rC ![]() 7cohS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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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 genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 26068.404 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 29957.627 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | Mass: 17179.646 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #5: Protein | Mass: 12453.081 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #6: Protein | Mass: 10684.038 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #7: Protein | Mass: 9549.802 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #8: Protein | Mass: 10039.244 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #9: Protein | Mass: 8494.982 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #10: Protein | Mass: 6682.726 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #11: Protein | Mass: 6365.217 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #12: Protein/peptide | Mass: 5449.396 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #13: Protein/peptide | Mass: 4967.756 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 1 types, 42 molecules ![](data/chem/img/DMU.gif)
#20: Sugar | ChemComp-DMU / |
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-Non-polymers , 14 types, 2092 molecules ![](data/chem/img/HEA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/LFA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/UNX.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/CA.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/LFA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/HOH.gif)
#14: Chemical | ChemComp-HEA / #15: Chemical | #16: Chemical | #17: Chemical | #18: Chemical | ChemComp-CDL / #19: Chemical | ChemComp-LFA / #21: Chemical | ChemComp-EDO / #22: Chemical | ChemComp-PGV / ( #23: Chemical | #24: Chemical | ChemComp-CHD / #25: Chemical | #26: Chemical | #27: Chemical | #28: 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: 4.04 Å3/Da / Density % sol: 69.58 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 6.8 Details: 40 mM sodium phosphate buffer, pH 6.8 0.2% (w/v) decyl-maltoside 1% (w/v) polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→200 Å / Num. obs: 684989 / % possible obs: 99.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 33.5 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.057 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 103025 / CC1/2: 0.758 / Rrim(I) all: 1.38 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7COH Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.058 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.772 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→40 Å
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Refine LS restraints |
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