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Yorodumi- PDB-6rgi: Partially unfolded cytochrome c in complex with sulfonatocalix[6]arene -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rgi | ||||||
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Title | Partially unfolded cytochrome c in complex with sulfonatocalix[6]arene | ||||||
Components | Cytochrome c iso-1 | ||||||
Keywords | ELECTRON TRANSPORT / molecular glues / calixarene / protein assembly / supramolecular chemistry | ||||||
Function / homology | Function and homology information Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding ...Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | ||||||
Authors | Engilberge, S. / Rennie, M.L. / Crowley, P.B. | ||||||
Funding support | Ireland, 1items
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Citation | Journal: Febs Lett. / Year: 2019 Title: Calixarene capture of partially unfolded cytochrome c. Authors: Engilberge, S. / Rennie, M.L. / Crowley, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rgi.cif.gz | 60 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rgi.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 6rgi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/6rgi ftp://data.pdbj.org/pub/pdb/validation_reports/rg/6rgi | HTTPS FTP |
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-Related structure data
Related structure data | 5lycS S: Starting model for refinement |
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Similar structure data |
-Links
-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.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CYC1, YJR048W, J1653 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044 |
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#2: Chemical | ChemComp-HEC / |
#3: Chemical | ChemComp-FWQ / |
#4: Chemical | ChemComp-IMD / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.7 Å3/Da / Density % sol: 65 % / Description: long rod |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 11 % PEG 8000, 0.1 M imidazole, 2 mM sulfonato-calix[6]arene |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.981 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.981 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→44.02 Å / Num. obs: 3582 / % possible obs: 91 % / Redundancy: 17.9 % / Biso Wilson estimate: 107.85 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.022 / Rrim(I) all: 0.094 / Net I/σ(I): 1.3 |
Reflection shell | Resolution: 2.64→2.94 Å / Rmerge(I) obs: 1.46 / Num. unique obs: 200 / Rpim(I) all: 0.482 / Rrim(I) all: 1.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LYC Resolution: 2.64→44.02 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.886 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 0.385
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Displacement parameters | Biso max: 218.42 Å2 / Biso mean: 93.18 Å2 / Biso min: 32.45 Å2
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Refine analyze | Luzzati coordinate error obs: 0.43 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.64→44.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.64→2.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: -31.9339 Å / Origin y: -8.5447 Å / Origin z: -5.307 Å
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Refinement TLS group | Selection details: { A|* } |