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Yorodumi- PDB-6nmp: SFX structure of oxidized cytochrome c oxidase at room temperature -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nmp | |||||||||||||||||||||||||||
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Title | SFX structure of oxidized cytochrome c oxidase at room temperature | |||||||||||||||||||||||||||
Components | (Cytochrome c oxidase subunit ...) x 13 | |||||||||||||||||||||||||||
Keywords | OXIDOREDUCTASE / complex IV / membrane protein / Terminal enzyme / electron transfer | |||||||||||||||||||||||||||
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||||||||||||||||||||
Authors | Rousseau, D.L. / Yeh, S.-R. / Ishigami, I. | |||||||||||||||||||||||||||
Funding support | United States, 8items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019 Title: Snapshot of an oxygen intermediate in the catalytic reaction of cytochromecoxidase. Authors: Ishigami, I. / Lewis-Ballester, A. / Echelmeier, A. / Brehm, G. / Zatsepin, N.A. / Grant, T.D. / Coe, J.D. / Lisova, S. / Nelson, G. / Zhang, S. / Dobson, Z.F. / Boutet, S. / Sierra, R.G. / ...Authors: Ishigami, I. / Lewis-Ballester, A. / Echelmeier, A. / Brehm, G. / Zatsepin, N.A. / Grant, T.D. / Coe, J.D. / Lisova, S. / Nelson, G. / Zhang, S. / Dobson, Z.F. / Boutet, S. / Sierra, R.G. / Batyuk, A. / Fromme, P. / Fromme, R. / Spence, J.C.H. / Ros, A. / 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 | 6nmp.cif.gz | 790.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nmp.ent.gz | 644.5 KB | Display | PDB format |
PDBx/mmJSON format | 6nmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/6nmp ftp://data.pdbj.org/pub/pdb/validation_reports/nm/6nmp | HTTPS FTP |
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-Related structure data
Related structure data | 6nknC 6nmfC 2dyrS C: citing same article (ref.) S: Starting model for refinement |
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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 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
#24: Sugar | ChemComp-DMU / |
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-Non-polymers , 14 types, 526 molecules
#14: Chemical | #15: Chemical | #16: Chemical | #17: Chemical | ChemComp-HEA / #18: Chemical | ChemComp-PGV / ( #19: Chemical | ChemComp-TGL / #20: Chemical | #21: Chemical | #22: Chemical | #23: Chemical | ChemComp-CHD / #25: Chemical | ChemComp-PEK / ( #26: Chemical | ChemComp-CDL / #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: 4.36 Å3/Da / Density % sol: 71.82 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 6.8 Details: 36 hour crystallization in a cold room with stirring |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.306 Å |
Detector | Type: CS-PAD XPP / Detector: PIXEL / Date: Dec 7, 2016 / Frequency: 120 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.306 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→15 Å / Num. obs: 150666 / % possible obs: 99.64 % / Redundancy: 204 % / CC1/2: 0.928 / Net I/σ(I): 2.8 |
Reflection shell | Resolution: 2.9→2.972 Å / Mean I/σ(I) obs: 0.43 / Num. unique obs: 10677 / CC1/2: 0.149 |
Serial crystallography measurement | Collimation: compound refractive lense / Pulse duration: 40 fsec. / Pulse photon energy: 9.5 keV / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Description: GCVN / Injector temperature: 293 K |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DYR Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 22.095 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R: 0.632 / ESU R Free: 0.329 / 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: 63.835 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→15 Å
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