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Yorodumi- PDB-5wau: Crystal Structure of CO-bound Cytochrome c Oxidase determined by ... -
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-Basic information
Entry | Database: PDB / ID: 5wau | |||||||||
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Title | Crystal Structure of CO-bound Cytochrome c Oxidase determined by Synchrotron X-Ray Crystallography at 100 K | |||||||||
Components | (Cytochrome c oxidase subunit ...) x 13 | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
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: 1.95 Å | |||||||||
Authors | Fromme, R. / Ishigami, I. / Yeh, S.Y. / Zatsepin, N. / Grant, T. / Fromme, P. / Rousseau, D. | |||||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature. Authors: Ishigami, I. / Zatsepin, N.A. / Hikita, M. / Conrad, C.E. / Nelson, G. / Coe, J.D. / Basu, S. / Grant, T.D. / Seaberg, M.H. / Sierra, R.G. / Hunter, M.S. / Fromme, P. / Fromme, R. / Yeh, S.R. / Rousseau, D.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wau.cif.gz | 822.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wau.ent.gz | 666.7 KB | Display | PDB format |
PDBx/mmJSON format | 5wau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/5wau ftp://data.pdbj.org/pub/pdb/validation_reports/wa/5wau | HTTPS FTP |
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-Related structure data
Related structure data | 5w97C 3ag1S 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 AaBbCcDdEeFfGgHhIiJjKkLlMm
#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
#25: Sugar | ChemComp-DMU / |
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-Non-polymers , 14 types, 1891 molecules
#14: Chemical | ChemComp-HEA / #15: Chemical | #16: Chemical | #17: Chemical | #18: Chemical | ChemComp-PGV / ( #19: Chemical | ChemComp-TGL / #20: Chemical | #21: Chemical | #22: Chemical | ChemComp-CHD / #23: Chemical | ChemComp-PEK / ( #24: Chemical | ChemComp-CDL / #26: Chemical | #27: Chemical | #28: Water | ChemComp-HOH / | |
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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: 4.13 Å3/Da / Density % sol: 70.19 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: .2 % decylmaltoside and 2.5 % PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→39 Å / Num. obs: 457753 / % possible obs: 94.33 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Net I/av σ(I): 12.67 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 0.93 / CC1/2: 0.518 / % possible all: 85.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AG1 Resolution: 1.95→39 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.664 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.135 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.528 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→39 Å
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