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Open data
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Basic information
Entry | Database: PDB / ID: 6pw0 | |||||||||
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Title | Cytochrome C oxidase delta 6 mutant | |||||||||
![]() | (Cytochrome c oxidase subunit ...) x 2 | |||||||||
![]() | OXIDOREDUCTASE / Oxidase / Proton pumping / Electron transfer / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / copper ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Liu, J. / Ferguson-Miller, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural changes at the surface of cytochrome c oxidase alter the proton-pumping stoichiometry. Authors: Berg, J. / Liu, J. / Svahn, E. / Ferguson-Miller, S. / Brzezinski, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 431.9 KB | Display | ![]() |
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PDB format | ![]() | 283.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6pw1C ![]() 2gsmS 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / End auth comp-ID: HIS / End label comp-ID: HIS
NCS ensembles :
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Components
-Cytochrome c oxidase subunit ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 62531.645 Da / Num. of mol.: 2 / Mutation: 6 residues were deleted at C-terminus Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: coxI, RSP_1877 / Production host: ![]() #2: Protein | Mass: 29365.385 Da / Num. of mol.: 2 / Mutation: 6 histidine tag added to the C-terminus Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: coxII, RSP_1826 / Production host: ![]() |
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-Sugars , 2 types, 11 molecules ![](data/chem/img/DMU.gif)
#3: Polysaccharide | #6: Sugar | ChemComp-DMU / |
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-Non-polymers , 10 types, 494 molecules ![](data/chem/img/OH.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/TRD.gif)
![](data/chem/img/HTH.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/TRD.gif)
![](data/chem/img/HTH.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-HEA / #7: Chemical | ChemComp-TRD / #8: Chemical | #9: Chemical | ChemComp-CU / #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-CD / #13: Chemical | ChemComp-TRS / | #14: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.13 Å3/Da / Density % sol: 70.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 100 mM MES, pH 6.3, 27 % PEG-400 2.5 % heptanetriol, 16 mM MgCl2, 0.65 mM CdCl2 and 0.013 % Dodecyl maltoside |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→42.84 Å / Num. obs: 117531 / % possible obs: 90 % / Redundancy: 5.7 % / Biso Wilson estimate: 46.81 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.491 / Num. unique obs: 7044 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GSM Resolution: 2.5→42.84 Å / SU ML: 0.2486 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0085
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→42.84 Å
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Refine LS restraints |
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LS refinement shell |
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