[English] 日本語
![](img/lk-miru.gif)
- PDB-6nmf: SFX structure of reduced cytochrome c oxidase at room temperature -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6nmf | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | SFX structure of reduced 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 / mitochondrial respiratory chain complex IV / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / mitochondrial respirasome ...TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / mitochondrial respiratory chain complex IV / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / mitochondrial respirasome / 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 | ![]()
| |||||||||||||||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 814.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 663.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 8.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 9.1 MB | Display | |
Data in XML | ![]() | 163.7 KB | Display | |
Data in CIF | ![]() | 208.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nknC ![]() 6nmpC ![]() 5b1bS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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) ![]() ![]() |
---|
-Sugars , 1 types, 4 molecules ![](data/chem/img/DMU.gif)
#24: Sugar | ChemComp-DMU / |
---|
-Non-polymers , 13 types, 792 molecules ![](data/chem/img/HEA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/TGL.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/PSC.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/TGL.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/CHD.gif)
![](data/chem/img/PSC.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#14: Chemical | ChemComp-HEA / #15: Chemical | #16: Chemical | #17: Chemical | #18: Chemical | ChemComp-PGV / ( #19: Chemical | ChemComp-TGL / #20: Chemical | ChemComp-CDL / #21: Chemical | #22: Chemical | ChemComp-CHD / #23: Chemical | #25: Chemical | ChemComp-PEK / ( #26: Chemical | #27: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.41 Å3/Da / Density % sol: 72.11 % |
---|---|
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 |
---|---|
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: 2.8→15 Å / Num. obs: 166575 / % possible obs: 99.27 % / Redundancy: 273 % / CC1/2: 0.971 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 2.8→2.87 Å / Mean I/σ(I) obs: 0.41 / Num. unique obs: 11900 / CC1/2: 0.15 / % possible all: 99.98 |
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: GDVN / Injector temperature: 293 K |
Serial crystallography data reduction | Crystal hits: 24101 / Frames indexed: 21962 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5B1B Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.935 / SU B: 18.056 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 72.918 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.8→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|