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- PDB-7bbt: Structure of cytochrome c in complex with a p-benzyl-sulfonato-ca... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bbt | |||||||||
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Title | Structure of cytochrome c in complex with a p-benzyl-sulfonato-calix[8]arene-PEG pseudorotaxane | |||||||||
![]() | Cytochrome c iso-1 | |||||||||
![]() | OXIDOREDUCTASE / extended-arm / molecular recognition / biohybrid / alpha-helix | |||||||||
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 / : / 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 / : / mitochondrial intermembrane space / electron transfer activity / heme binding / mitochondrion / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mockler, N.M. / Ramberg, K. / Guagnini, F. / Raston, C.L. / Crowley, P.B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Noncovalent Protein-Pseudorotaxane Assembly Incorporating an Extended Arm Calix[8]arene with alpha-Helical Recognition Properties. Authors: Mockler, N.M. / Ramberg, K.O. / Guagnini, F. / Raston, C.L. / 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 | ![]() | 119.3 KB | Display | ![]() |
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PDB format | ![]() | 92.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.6 MB | Display | ![]() |
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Full document | ![]() | 3.6 MB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rslS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 12041.770 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-HEC / #3: Chemical | #4: Chemical | ChemComp-15P / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 3350 200mM Ammonium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 21, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98009 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.02→50.57 Å / Num. obs: 10928 / % possible obs: 96.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 90.54 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.093 / Rrim(I) all: 0.241 / Net I/σ(I): 8.9 / Num. measured all: 73389 / Scaling rejects: 2369 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6RSL Resolution: 3.023→50.57 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.86 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.479
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Displacement parameters | Biso max: 114.35 Å2 / Biso mean: 75.3 Å2 / Biso min: 26.66 Å2
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Refine analyze | Luzzati coordinate error obs: 0.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.023→50.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.023→3.06 Å / Rfactor Rfree error: 0
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