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- PDB-6nkn: Time-resolved SFX structure of the PR intermediate of cytochrome ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nkn | |||||||||||||||||||||||||||
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Title | Time-resolved SFX structure of the PR intermediate of cytochrome c oxidase at room temperature | |||||||||||||||||||||||||||
![]() | (Cytochrome c oxidase subunit ...) x 13 | |||||||||||||||||||||||||||
![]() | OXIDOREDUCTASE / complex IV / membrane protein / Terminal enzyme / electron transfer | |||||||||||||||||||||||||||
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 | ![]() ![]() ![]() | |||||||||||||||||||||||||||
![]() | Rousseau, D.L. / Yeh, S.-R. / Ishigami, I. | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 797.5 KB | Display | ![]() |
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PDB format | ![]() | 650 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 9.5 MB | Display | ![]() |
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Full document | ![]() | 9.7 MB | Display | |
Data in XML | ![]() | 163.5 KB | Display | |
Data in CIF | ![]() | 208.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nmfC ![]() 6nmpC ![]() 2dyrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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, 4 molecules ![](data/chem/img/DMU.gif)
#28: Sugar | ChemComp-DMU / |
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-Non-polymers , 15 types, 824 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/TGL.gif)
![](data/chem/img/O.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/PSC.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/TGL.gif)
![](data/chem/img/O.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/PSC.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#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 | #24: Chemical | ChemComp-CHD / #25: Chemical | ChemComp-PEK / ( #26: Chemical | ChemComp-CDL / #27: Chemical | #29: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72.05 % |
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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: ![]() ![]() ![]() |
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: 2.5→10.5 Å / Num. obs: 231448 / % possible obs: 98.54 % / Redundancy: 1038 % / CC1/2: 0.989 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.5→2.561 Å / Mean I/σ(I) obs: 0.56 / Num. unique obs: 16305 / CC1/2: 0.168 / % possible all: 100 |
Serial crystallography measurement | Collimation: compound refractive lense / Pulse duration: 40 fsec. / Pulse energy: 3000 µJ / Pulse photon energy: 9.5 keV / Source size: 9 µm2 / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Description: GDVN / Injector temperature: 293 K |
Serial crystallography data reduction | Crystal hits: 108241 / Frames indexed: 98993 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2dyr Resolution: 2.5→10.5 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 11.068 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.205 / 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: 63.44 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→10.5 Å
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Refine LS restraints |
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