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- PDB-6gd6: Cytochrome c in complex with Sulfonato-calix[8]arene, H3 form wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gd6 | ||||||
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Title | Cytochrome c in complex with Sulfonato-calix[8]arene, H3 form with ammonium sulfate | ||||||
![]() | Cytochrome c iso-1 | ||||||
![]() | OXIDOREDUCTASE / calixarene / scaffold / supramolecular / assembly | ||||||
Function / homology | ![]() Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding ...Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Rennie, M.L. / Fox, G.C. / Crowley, P.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Auto-regulated Protein Assembly on a Supramolecular Scaffold. Authors: Rennie, M.L. / Fox, G.C. / Perez, J. / Crowley, P.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.4 KB | Display | ![]() |
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PDB format | ![]() | 63 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gd7C ![]() 6gd8C ![]() 6gd9C ![]() 5lycS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 12041.770 Da / Num. of mol.: 1 / Mutation: C102T, T-5A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CYC1, YJR048W, J1653 / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-HEC / | ||
#3: Chemical | ChemComp-EVB / | ||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Description: large red/pink rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.75 M ammonium sulfate 0.2 M NaCl (2x protein solution : 1x crystallisation condition) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 9, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.2→35.68 Å / Num. obs: 64600 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.032 / Rrim(I) all: 0.064 / Net I/σ(I): 9.9 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LYC chain A Resolution: 1.2→35.68 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.86 / SU ML: 0.017 / SU R Cruickshank DPI: 0.0248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.025 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.31 Å2 / Biso mean: 18.231 Å2 / Biso min: 9.32 Å2
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Refinement step | Cycle: final / Resolution: 1.2→35.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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