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Yorodumi- PDB-6rsk: Cytochrome c co-crystallized with 20 eq. sulfonato-calix[8]arene ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rsk | ||||||
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Title | Cytochrome c co-crystallized with 20 eq. sulfonato-calix[8]arene and 15 eq. spermine - structure II | ||||||
Components | Cytochrome c iso-1 | ||||||
Keywords | OXIDOREDUCTASE / Molecular glues / Molecular switch / spermine / polyamine / calixarene / supramolecular chemistry | ||||||
Function / homology | Function and homology information Release of apoptotic factors from the mitochondria / Pyroptosis / 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 ...Release of apoptotic factors from the mitochondria / Pyroptosis / 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 S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Engilberge, S. / Crowley, P.B. | ||||||
Funding support | Ireland, 1items
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Citation | Journal: Acs Nano / Year: 2019 Title: Tuning Protein Frameworks via Auxiliary Supramolecular Interactions. Authors: Engilberge, S. / Rennie, M.L. / Dumont, E. / 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 | 6rsk.cif.gz | 141.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rsk.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 6rsk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/6rsk ftp://data.pdbj.org/pub/pdb/validation_reports/rs/6rsk | HTTPS FTP |
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-Related structure data
Related structure data | 6gdaC 6rsiC 6rsjC 6rslC 6gd9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 12041.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: CYC1, YJR048W, J1653 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044 |
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-Non-polymers , 5 types, 202 molecules
#2: Chemical | #3: Chemical | ChemComp-EVB / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-SPM / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.69 Å3/Da / Density % sol: 70 % / Description: red cubic crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES pH 7.5, 0.15 M NaCl, 2.2 M Ammonium sulfate, 0.04 M sulfonato-calix[8]arene, 0.03 M spermine |
-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: 0.97624 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 2.306→71.035 Å / Num. obs: 20779 / % possible obs: 100 % / Redundancy: 25.9 % / Biso Wilson estimate: 53.26 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.039 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.306→2.346 Å / Rmerge(I) obs: 1.871 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1006 / CC1/2: 0.748 / Rpim(I) all: 0.358 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GD9 Resolution: 2.31→66.84 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.368 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.243 / SU Rfree Blow DPI: 0.191 / SU Rfree Cruickshank DPI: 0.181
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Displacement parameters | Biso mean: 60.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.31→66.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.31→2.32 Å / Total num. of bins used: 50
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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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