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- PDB-3omi: Catalytic core subunits (I and II) of cytochrome C oxidase from R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3omi | ||||||
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Title | Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with D132A mutation | ||||||
![]() | (Cytochrome c ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / TRANSMEMBRANE PROTEIN COMPLEX | ||||||
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. / Qin, L. / Ferguson-Miller, S. | ||||||
![]() | ![]() Title: Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump. Authors: Liu, J. / Qin, L. / Ferguson-Miller, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 340.1 KB | Display | ![]() |
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PDB format | ![]() | 284.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Cytochrome c ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 59496.344 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 17-551 / Mutation: D132A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 17023/2.4.1/NCIB 8253/DSM 158 / Gene: coxI, CTAD, RHOS4_04590, RSP_1877 / Plasmid: pRK415-1 / Production host: ![]() #2: Protein | Mass: 28617.637 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 30-281 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 17023/2.4.1/NCIB 8253/DSM 158 / Gene: coxII, CTAB, CTAC, RHOS4_04060, RSP_1826 / Plasmid: pRK415-1 / Production host: ![]() |
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-Sugars , 1 types, 11 molecules ![](data/chem/img/DMU.gif)
#4: Sugar | ChemComp-DMU / |
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-Non-polymers , 11 types, 523 molecules ![](data/chem/img/OH.gif)
![](data/chem/img/TRD.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HTH.gif)
![](data/chem/img/CU1.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRD.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HTH.gif)
![](data/chem/img/CU1.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #5: Chemical | ChemComp-TRD / #6: Chemical | ChemComp-HEA / #7: Chemical | ChemComp-CU / #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-HTH / ( | #12: Chemical | #13: Chemical | ChemComp-CD / #14: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | LIGANDS LABELLED AS TRD ARE ALL ALKYL CHAINS WITH DIFFERENT LENGTHS OF EITHER DMU OR NATIVE ...LIGANDS LABELLED AS TRD ARE ALL ALKYL CHAINS WITH DIFFERENT LENGTHS OF EITHER DMU OR NATIVE MEMBRANE LIPIDS SUCH AS PHOSPHATID |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 69.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 26-29% PEG 400, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K, vapor diffusion, sitting drop |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond / Protocol: SINGLE WEAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→50 Å / Num. obs: 151816 / % possible obs: 97.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 12 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Details: THERE IS RESIDUAL DENSITY IN (FO-FC) DIFFERENCE FOURIER MAP AT THE MAGNESIUM SITES IN BOTH MOLECULES AND THE B-FACTOR FOR EACH MAGNESIUM ION IS UNUSUALLY LOW. THESE OBSERVATIONS SUGGEST THAT ...Details: THERE IS RESIDUAL DENSITY IN (FO-FC) DIFFERENCE FOURIER MAP AT THE MAGNESIUM SITES IN BOTH MOLECULES AND THE B-FACTOR FOR EACH MAGNESIUM ION IS UNUSUALLY LOW. THESE OBSERVATIONS SUGGEST THAT THIS MAGNESIUM SITE MAY BE PARTIALLY OCCUPIED BY A HEAVIER META ION IN THE PROTEIN CRYSTAL. THERE ARE RESIDUAL DENSITIES IN (FO-FC) DIFFERENCE FOURIER MAP AT THE SITE OF CU AND HEMEA FE. THESE DENSITIES SUGGEST THAT THE METEAL CENTER OF THIS MUTATNT MIGHT BE IN A STATE DIFFERENT FROM WILD TYPE IN CRYSTAL.
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→35.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.21 Å
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