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Yorodumi- PDB-2b11: Crystal structure of the protein-protein complex between F82W cyt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b11 | |||||||||
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Title | Crystal structure of the protein-protein complex between F82W cytochrome c and cytochrome c peroxidase | |||||||||
Components |
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Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / cytochrome / electron transfer / OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX | |||||||||
Function / homology | Function and homology information Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cytochrome-c peroxidase / cardiolipin binding / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : ...Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cytochrome-c peroxidase / cardiolipin binding / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Kang, S.A. / Crane, B.R. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 Title: Effects of interface mutations on association modes and electron-transfer rates between proteins Authors: Kang, S.A. / Crane, B.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b11.cif.gz | 185.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b11.ent.gz | 152 KB | Display | PDB format |
PDBx/mmJSON format | 2b11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b11_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 2b11_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2b11_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 2b11_validation.cif.gz | 54.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/2b11 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/2b11 | 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
#1: Protein | Mass: 33571.238 Da / Num. of mol.: 2 / Mutation: F82W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CCP1, CCP, CPO / Production host: Escherichia coli (E. coli) / References: UniProt: P00431, cytochrome-c peroxidase #2: Protein | Mass: 12112.870 Da / Num. of mol.: 2 / Mutation: F82W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CYC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044 #3: Chemical | #4: Chemical | #5: 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: 2.3 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 3350, NaCl, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→30 Å / Num. obs: 37320 / % possible obs: 95.5 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.136 / Χ2: 1.916 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / σ(F): 0
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Solvent computation | Bsol: 37.619 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.109 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Xplor file |
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