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- PDB-7y44: Re-refinement of damage free X-ray structure of bovine cytochrome... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7y44 | ||||||
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Title | Re-refinement of damage free X-ray structure of bovine cytochrome c oxidase at 1.9 angstrom resolution | ||||||
![]() | (Cytochrome c oxidase subunit ...) x 13 | ||||||
![]() | OXIDOREDUCTASE / respiratory enzyme / membrane protein / heme protein | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Tsukihara, T. / Hirata, K. / Ago, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL. Authors: Hirata, K. / Shinzawa-Itoh, K. / Yano, N. / Takemura, S. / Kato, K. / Hatanaka, M. / Muramoto, K. / Kawahara, T. / Tsukihara, T. / Yamashita, E. / Tono, K. / Ueno, G. / Hikima, T. / ...Authors: Hirata, K. / Shinzawa-Itoh, K. / Yano, N. / Takemura, S. / Kato, K. / Hatanaka, M. / Muramoto, K. / Kawahara, T. / Tsukihara, T. / Yamashita, E. / Tono, K. / Ueno, G. / Hikima, T. / Murakami, H. / Inubushi, Y. / Yabashi, M. / Ishikawa, T. / Yamamoto, M. / Ogura, T. / Sugimoto, H. / Shen, J.R. / Yoshikawa, S. / Ago, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 13.5 MB | Display | ![]() |
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Full document | ![]() | 13.8 MB | Display | |
Data in XML | ![]() | 200.3 KB | Display | |
Data in CIF | ![]() | 259.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wg7C ![]() 2dyrS 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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1 | ![]()
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2 | ![]()
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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) ![]() ![]() #2: Protein | Mass: 26068.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 29957.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 17179.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 12453.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 9629.782 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 10039.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 8537.019 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 6682.726 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | Mass: 6365.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein/peptide | Mass: 5449.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein/peptide | Mass: 4967.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 1 types, 23 molecules ![](data/chem/img/DMU.gif)
#21: Sugar | ChemComp-DMU / |
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-Non-polymers , 16 types, 2481 molecules ![](data/chem/img/HEA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TGL.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/PSC.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TGL.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/PSC.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#14: Chemical | ChemComp-HEA / #15: Chemical | #16: Chemical | #17: Chemical | ChemComp-NA / #18: Chemical | #19: Chemical | ChemComp-PGV / ( #20: Chemical | ChemComp-EDO / #22: Chemical | ChemComp-TGL / #23: Chemical | #24: Chemical | #25: Chemical | ChemComp-PEK / ( #26: Chemical | ChemComp-CDL / #27: Chemical | ChemComp-CHD / #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: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.69 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 5.7 Details: 40mM sodium phosphate buffer, 0.2% decylmaltoside, 1% PEG 4000, 2% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.241 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→27.33 Å / Num. obs: 500669 / % possible obs: 96.2 % / Redundancy: 3.8 % / CC1/2: 0.872 / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.137 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 71920 / Rpim(I) all: 0.232 / % possible all: 95.1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2DYR Resolution: 1.9→27.312 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.78 / 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: 1.9→27.312 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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