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- PDB-1m57: Structure of cytochrome c oxidase from Rhodobacter sphaeroides (E... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m57 | |||||||||
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Title | Structure of cytochrome c oxidase from Rhodobacter sphaeroides (EQ(I-286) mutant)) | |||||||||
![]() | (CYTOCHROME C ...![]() | |||||||||
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Function / homology | ![]() respiratory chain complex IV / aerobic electron transport chain / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Svensson-Ek, M. / Abramson, J. / Larsson, G. / Tornroth, S. / Brezezinski, P. / Iwata, S. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 478.6 KB | Display | ![]() |
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PDB format | ![]() | 397.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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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: 63194.398 Da / Num. of mol.: 2 / Mutation: E286Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein | ![]() Mass: 29385.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Protein | ![]() Mass: 30197.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #4: Protein | ![]() Mass: 5409.267 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 462 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.91 Å3/Da / Density % sol: 68.54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: ![]() ![]() ![]() |
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![]() |
Reflection | Resolution: 3→40 Å / Num. all: 71181 / Num. obs: 163199 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 3→3.11 Å / % possible all: 90 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 71181 / Num. measured all: 163199 / Rmerge(I) obs: 0.124 |
Reflection shell | *PLUS Highest resolution: 3 Å / % possible obs: 90 % / Num. unique obs: 6553 / Num. measured obs: 27418 / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.1 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Refinement step | Cycle: LAST / Resolution: 3→4 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 40 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |