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Yorodumi- PDB-1m56: Structure of cytochrome c oxidase from Rhodobactor sphaeroides (W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m56 | |||||||||
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Title | Structure of cytochrome c oxidase from Rhodobactor sphaeroides (Wild Type) | |||||||||
Components | (CYTOCHROME C ...) x 4 | |||||||||
Keywords | OXIDOREDUCTASE / Membrane Protein | |||||||||
Function / homology | Function and homology information aerobic electron transport chain / 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 ...aerobic electron transport chain / 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 / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rhodobacter sphaeroides (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Svensson-Ek, M. / Abramson, J. / Larsson, G. / Tornroth, S. / Brezezinski, P. / Iwata, S. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides. Authors: Svensson-Ek, M. / Abramson, J. / Larsson, G. / Tornroth, S. / Brzezinski, P. / Iwata, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m56.cif.gz | 476.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m56.ent.gz | 397.6 KB | Display | PDB format |
PDBx/mmJSON format | 1m56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m56_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1m56_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1m56_validation.xml.gz | 79.4 KB | Display | |
Data in CIF | 1m56_validation.cif.gz | 108.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/1m56 ftp://data.pdbj.org/pub/pdb/validation_reports/m5/1m56 | 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 ... , 4 types, 8 molecules AGBHCIDJ
#1: Protein | Mass: 63195.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P33517, cytochrome-c oxidase #2: Protein | Mass: 29385.436 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: Q03736, cytochrome-c oxidase #3: Protein | Mass: 30197.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P84153, cytochrome-c oxidase #4: Protein | Mass: 5409.267 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: Q8KRK5, cytochrome-c oxidase |
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-Non-polymers , 6 types, 462 molecules
#5: Chemical | ChemComp-CU / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-HEA / #9: Chemical | ChemComp-3PE / #10: 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: 68.44 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 1998 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. all: 119260 / Num. obs: 232383 / % possible obs: 69.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.3→2.4 Å / % possible all: 36 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 119260 / Num. measured all: 232383 / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / % possible obs: 36 % / Num. unique obs: 7880 / Num. measured obs: 20048 / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 40 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |