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Yorodumi- PDB-2gsm: Catalytic Core (Subunits I and II) of Cytochrome c oxidase from R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gsm | ||||||
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Title | Catalytic Core (Subunits I and II) of Cytochrome c oxidase from Rhodobacter sphaeroides | ||||||
Components | (Cytochrome c oxidase subunit ...) 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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Qin, L. / Hiser, C. / Mulichak, A. / Garavito, R.M. / Ferguson-Miller, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Identification of conserved lipid/detergent-binding sites in a high-resolution structure of the membrane protein cytochrome c oxidase. Authors: Qin, L. / Hiser, C. / Mulichak, A. / Garavito, R.M. / 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 | 2gsm.cif.gz | 342.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gsm.ent.gz | 288.1 KB | Display | PDB format |
PDBx/mmJSON format | 2gsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/2gsm ftp://data.pdbj.org/pub/pdb/validation_reports/gs/2gsm | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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 / Production host: Rhodobacter sphaeroides (bacteria) / 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 / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: Q03736, cytochrome-c oxidase |
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-Sugars , 1 types, 10 molecules
#3: Sugar | ChemComp-DMU / |
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-Non-polymers , 8 types, 535 molecules
#4: Chemical | ChemComp-CU / #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-HEA / #9: Chemical | ChemComp-TRD / #10: Chemical | ChemComp-CD / #11: 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: 3.93 Å3/Da / Density % sol: 68.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: PEG-400, 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: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 30, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 192300 / Num. obs: 184839 / % possible obs: 96.12 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2→2.051 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.8 / Num. unique all: 13648 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.77 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.129 / 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 RESOLVED BEYOND CB ATOMS. THESE 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 ARG B 131 HIS B 284 PHE C 17 THR C 18 ARG C 19 LYS C 74 ARG C 137 LYS C 224 ARG C 521 ARG C 524 LYS D 86 ARG D 131 HIS D 284. (4) THE DISTAL GLUCOSE RING OF THE FOLLOWING DELCYL MALTOSIDE MOLECULES ARE NOT RESOLVED. THESE UNRESOLVED ATOMS ARE ASSIGNED AN OCCUPANCY OF 0.00 AND AN ARBITORY B-FACTOR OF 100.00: DMU 5004 DMU 6004. (5) 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 sugars labelled as DMU do not contain the carbon chain. 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.504 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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