+Open data
-Basic information
Entry | Database: PDB / ID: 5t8w | ||||||
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Title | Cytochrome c - calixarene free | ||||||
Components | Cyc1p | ||||||
Keywords | ELECTRON TRANSPORT / cytochrome c / P212121 | ||||||
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 / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Doolan, A.M. / Rennie, M.L. / Crowley, P.B. | ||||||
Funding support | Ireland, 1items
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Citation | Journal: Chemistry / Year: 2018 Title: Protein Recognition by Functionalized Sulfonatocalix[4]arenes. Authors: Doolan, A.M. / 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 | 5t8w.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t8w.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 5t8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/5t8w ftp://data.pdbj.org/pub/pdb/validation_reports/t8/5t8w | HTTPS FTP |
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-Related structure data
Related structure data | 5kpfC 5lftC 3tyiS C: citing same article (ref.) 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.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CYC1, H834_YJM1574J00260 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C6AZG8, UniProt: P00044*PLUS #2: Chemical | #3: Chemical | #4: 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: 1.99 Å3/Da / Density % sol: 38.26 % |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion, sitting drop Details: 0.3 uL of 1.2 mM cytochrome c and 8 mM phenyl-trisulfonato-calix[4]arene 0.15 uL reservoir solution (20 mM PEG 3350, 200 mM ammonium chloride pH 6.3) 0.1 uL seed solution (from 3TYI crystals) |
-Data collection
Diffraction | Mean temperature: 123 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→48.08 Å / Num. obs: 26212 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.036 / Rrim(I) all: 0.071 / Net I/σ(I): 12.9 / Num. measured all: 96391 / Scaling rejects: 64 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TYI Resolution: 1.6→48.077 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.24 Å2 / Biso mean: 20.2027 Å2 / Biso min: 9.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→48.077 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %
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