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Yorodumi- PDB-3oma: Catalytic core subunits (I and II) of cytochrome C oxidase from R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oma | ||||||
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Title | Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with K362M mutation | ||||||
Components | (Cytochrome c ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / TRANSMEMBRANE PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information 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 | Rhodobacter sphaeroides 2.4.1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Liu, J. / Qin, L. / Ferguson-Miller, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oma.cif.gz | 340.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oma.ent.gz | 283.9 KB | Display | PDB format |
PDBx/mmJSON format | 3oma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oma_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 3oma_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 3oma_validation.xml.gz | 64.2 KB | Display | |
Data in CIF | 3oma_validation.cif.gz | 87.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/3oma ftp://data.pdbj.org/pub/pdb/validation_reports/om/3oma | HTTPS FTP |
-Related structure data
-Links
-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: 59542.367 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 17-551 / Mutation: K362M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria) Strain: ATCC 17023/2.4.1/NCIB 8253/DSM 158 / Gene: coxI, CTAD, RHOS4_04590, RSP_1877 / Plasmid: pRK415-1 / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: Q3J5A7, cytochrome-c oxidase #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.) Rhodobacter sphaeroides 2.4.1 (bacteria) Strain: ATCC 17023/2.4.1/NCIB 8253/DSM 158 / Gene: coxII, CTAB, CTAC, RHOS4_04060, RSP_1826 / Plasmid: pRK415-1 / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: Q3J5G0, cytochrome-c oxidase |
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-Sugars , 1 types, 11 molecules
#4: Sugar | ChemComp-DMU / |
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-Non-polymers , 10 types, 482 molecules
#3: Chemical | #5: Chemical | ChemComp-TRD / #6: Chemical | ChemComp-HEA / #7: Chemical | ChemComp-CU / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-HTH / ( | #11: Chemical | #12: Chemical | ChemComp-CD / #13: 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.12 Å3/Da / Density % sol: 70.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 26-28% 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: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 12, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond / Protocol: SINGLE WEAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→50 Å / Num. obs: 145094 / % possible obs: 92 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.059 / Χ2: 1.018 / Net I/σ(I): 13.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.1914 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8647 / SU B: 4.58 / SU ML: 0.113 / SU R Cruickshank DPI: 0.1976 / SU Rfree: 0.1696 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.17 / 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 max: 102.95 Å2 / Biso mean: 47.1316 Å2 / Biso min: 20.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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