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- PDB-6gd7: Cytochrome c in complex with Sulfonato-calix[8]arene, H3 form with PEG -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gd7 | ||||||
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Title | Cytochrome c in complex with Sulfonato-calix[8]arene, H3 form with PEG | ||||||
![]() | Cytochrome c iso-1 | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() Release of apoptotic factors from the mitochondria / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 74.8 KB | Display | ![]() |
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PDB format | ![]() | 52.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6gd6C ![]() 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-GOL / ![]() |
#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, sitting drop Details: 5 % PEG 3350 (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![]() |
Reflection | Resolution: 1.55→40.71 Å / Num. obs: 29520 / % possible obs: 99.9 % / Redundancy: 4.4 % / CC1/2: 1 / Rpim(I) all: 0.026 / Rrim(I) all: 0.056 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 3.9 % / Num. unique obs: 1434 / CC1/2: 0.49 / Rpim(I) all: 0.256 / Rrim(I) all: 0.516 / % possible all: 99.9 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: 5LYC chain A Resolution: 1.55→40.71 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.896 / SU ML: 0.047 / SU R Cruickshank DPI: 0.0625 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.061 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: 72.01 Å2 / Biso mean: 30.532 Å2 / Biso min: 15.66 Å2
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Refinement step | Cycle: final / Resolution: 1.55→40.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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