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Yorodumi- PDB-3fyi: Catalytic core subunits (I and II) of cytochrome C oxidase from R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fyi | ||||||
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Title | Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides in the reduced state bound with cyanide | ||||||
Components | (Cytochrome c oxidase subunit ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / conformational changes / cyanide binding / Cell membrane / 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: 2.2 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 | 3fyi.cif.gz | 351.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fyi.ent.gz | 282.7 KB | Display | PDB format |
PDBx/mmJSON format | 3fyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fyi_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 3fyi_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 3fyi_validation.xml.gz | 64.6 KB | Display | |
Data in CIF | 3fyi_validation.cif.gz | 88.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/3fyi ftp://data.pdbj.org/pub/pdb/validation_reports/fy/3fyi | HTTPS FTP |
-Related structure data
Related structure data | 3fyeC 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, 503 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: 68.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 23%-24% PEG-400, crystals reduced with dithionite and soaked with cyanide, 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: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 145489 / % possible obs: 95.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.072 |
Reflection shell | Resolution: 2.2→2.257 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.52 / % possible all: 73.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GSM Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.002 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.155 / 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 GLU-A-548 GLU-B-131 LYS-C-74 ARG-C- 137 LYS-C-224 ARG-C-521 ARG-C-524 GLU-C-548 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 CHAINS, OR THE DISTAL GLUCOSE MOIETY. THE AUTHORS DO NOT KNOW FOR SURE THE IDENTITIES OF THE COMPLETE MOLECULES YET.
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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 mean: 44.024 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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