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Yorodumi- PDB-3fye: Catalytic core subunits (I and II) of cytochrome c oxidase from R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fye | ||||||
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Title | Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides in the reduced state | ||||||
Components | (Cytochrome C oxidase subunit ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / conformational changes / Cell membrane / Copper / Electron transport / Heme / Hydrogen ion transport / Ion transport / Iron / Membrane / Metal-binding / Respiratory chain / Transmembrane / Transport | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Qin, L. / Mills, D.A. / Proshlyakov, D.A. / Hiser, C. / Ferguson-Miller, S. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Redox dependent conformational changes in cytochrome c oxidase suggest a gating mechanism for proton uptake. Authors: Qin, L. / Liu, J. / Mills, D. / Proshlyakov, D.A. / Hiser, C. / 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 | 3fye.cif.gz | 350.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fye.ent.gz | 282.6 KB | Display | PDB format |
PDBx/mmJSON format | 3fye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fye_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 3fye_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 3fye_validation.xml.gz | 64.9 KB | Display | |
Data in CIF | 3fye_validation.cif.gz | 88.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/3fye ftp://data.pdbj.org/pub/pdb/validation_reports/fy/3fye | HTTPS FTP |
-Related structure data
Related structure data | 3fyiC 2gsmS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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 oxidase subunit ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 63195.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: ctaD / Plasmid: PRK415 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): deltaIdeltaIV / References: UniProt: P33517, cytochrome-c oxidase #2: Protein | Mass: 29365.385 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: ctaC, coxII, ctaB / Plasmid: PRK415 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): deltaIdeltaIV / References: UniProt: Q03736, cytochrome-c oxidase |
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-Sugars , 1 types, 10 molecules
#8: Sugar | ChemComp-DMU / |
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-Non-polymers , 9 types, 513 molecules
#3: Chemical | ChemComp-HEA / #4: Chemical | ChemComp-CU1 / #5: Chemical | #6: Chemical | #7: Chemical | #9: Chemical | ChemComp-TRD / #10: Chemical | ChemComp-HTO / | #11: Chemical | ChemComp-CD / #12: Water | ChemComp-HOH / | |
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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: 3.9 Å3/Da / Density % sol: 68.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 23-24% PEG-400, crystal reduced by dithionite, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→50 Å / Num. obs: 162159 / % possible obs: 98.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.066 / Χ2: 1.006 |
Reflection shell | Resolution: 2.15→2.206 Å / Redundancy: 4 % / Rmerge(I) obs: 0.606 / Num. unique all: 10331 / Χ2: 0.963 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GSM Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.069 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: (1) THERE IS A COVALENT LINKAGE BETWEEN NE2 OF HIS284 OF SUBUNIT I AND CE2 OF TYR288 OF SUBUNIT I. (2) THERE IS RESIDUAL DENSITY IN (FO-FC) DIFFERENCE FOURIER MAP AT THE MAGNESIUM SITES IN ...Details: (1) THERE IS A COVALENT LINKAGE BETWEEN NE2 OF HIS284 OF SUBUNIT I AND CE2 OF TYR288 OF SUBUNIT I. (2) 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 METAL ION IN THE PROTEIN CRYSTAL. (3) THE SIDE CHAINS OF THE FOLLOWING RESIDUES ARE NOT FULLY RESOLVED. THE UNRESOLVED SIDE CHAIN ATOMS ARE ASSIGNED AN OCCUPANCY OF 0.00 AND AN ARBITORY B-FACTOR OF 100.00: PHE-A-17 THR-A-18 ARG-A-19 LYS-A-74 LYS-A-224 GLU-A-548 LYS-B-86 GLU-B-131 LYS-C-74 ARG-C-137 LYS-C-224 GLU-C-548 HIS-C-549 LYS-D-86 HIS-D-284 (4) LIGANDS LABELLED AS TRD ARE ALL ALKYL CHAINS (WITH DIFFERENT LENGTHS) OF EITHER DMU OR NATIVE MEMBRANE LIPIDS SUCH AS PHOSPHATIDYL ETHANOLAMINE OR CARDIOLIPIN. SOME OF THE DETERGENTS LABELLED AS DMU DO NOT CONTAIN THE CARBON CHAIN, OR THE DISTAL GLUCOSE MOIETY. THE AUTHORS DO NOT KNOW FOR SURE THE IDENTITIES OF THE COMPLETE MOLECULES YET. (5) THERE IS AN UNKOWN ATOM OR ION NEAR HIS26 AND THR550 OF SUBUNIT I.
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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: 100.92 Å2 / Biso mean: 45.8 Å2 / Biso min: 9.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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