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- PDB-6y0j: Cytochrome c in complex with phosphonato-calix[6]arene and sulfon... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y0j | ||||||
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Title | Cytochrome c in complex with phosphonato-calix[6]arene and sulfonato-calix[8]arene | ||||||
![]() | Cytochrome c iso-1 | ||||||
![]() | OXIDOREDUCTASE / Molecular glue / calixarene / protein assembly / framework / supramolecular chemistry | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Engilberge, S. / Rennie, M.L. / Crowley, P.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Protein-macrocycle framework engineering: supramolecular copolymerisation with two disparate calixarenes Authors: Mockler, N.M. / Engilberge, S. / Rennie, M.L. / 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 | ![]() | 220.6 KB | Display | ![]() |
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PDB format | ![]() | 178 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tyiS 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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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 | ChemComp-7AZ / #4: Chemical | #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: 5.12 Å3/Da / Density % sol: 73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 10 % PEG 8000, 8 % ethylene glycol, 100 mM HEPES pH 7.5 |
-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: Jan 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98008 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→62.31 Å / Num. obs: 16206 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 56.24 Å2 / CC1/2: 0.939 / Rmerge(I) obs: 0.704 / Rpim(I) all: 0.163 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.7→3.05 Å / Num. unique obs: 810 / CC1/2: 0.097 / Rpim(I) all: 0.592 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TYI Resolution: 2.7→62.31 Å / Cor.coef. Fo:Fc: 0.769 / Cor.coef. Fo:Fc free: 0.74 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.419
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Displacement parameters | Biso max: 147.5 Å2 / Biso mean: 60.16 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.51 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→62.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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