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Yorodumi- PDB-5kpf: Crystal structure of cytochrome c - Phenyl-trisulfonatocalix[4]ar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kpf | ||||||
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Title | Crystal structure of cytochrome c - Phenyl-trisulfonatocalix[4]arene complex | ||||||
Components | Cytochrome c iso-1 | ||||||
Keywords | ELECTRON TRANSPORT / cytochrome c / modified calixarene / phenyl group | ||||||
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: 1.698 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 | 5kpf.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kpf.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 5kpf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/5kpf ftp://data.pdbj.org/pub/pdb/validation_reports/kp/5kpf | HTTPS FTP |
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-Related structure data
Related structure data | 5lftC 5t8wC 3tyiS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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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, YJR048W, J1653 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044 #2: Chemical | #3: Chemical | ChemComp-NO3 / | #4: Chemical | ChemComp-6VJ / | #5: 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: 1.89 Å3/Da / Density % sol: 34.99 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 20 mM PEG 3350, 200 mM Ammonium Nitrate pH 6.3 cyt c-sclx4 seed (grown in 18% PEG 8000, 50 mM NaCl, 100 mM MgCl2, 50 mM NaOAc pH 5.6) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 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: 0.9786 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.698→86.701 Å / Num. all: 20722 / Num. obs: 20722 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 16.89 Å2 / Rpim(I) all: 0.057 / Rrim(I) all: 0.152 / Rsym value: 0.14 / Net I/av σ(I): 4.371 / Net I/σ(I): 9.1 / Num. measured all: 145765 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.698→43.351 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.23 Å2 / Biso mean: 20.1775 Å2 / Biso min: 8.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.698→43.351 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: 8
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