[English] 日本語
Yorodumi- PDB-7pr4: Cocrystal Form II of a cytochrome c, sulfonato-thiacalix[4]arene ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pr4 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cocrystal Form II of a cytochrome c, sulfonato-thiacalix[4]arene - zinc cluster | ||||||||||||
Components | Cytochrome c iso-1 | ||||||||||||
Keywords | ELECTRON TRANSPORT / calixarene / molecular glue / synthetic receptor / alpha helix / thiacalixarene / metal cluster | ||||||||||||
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: 1.32 Å | ||||||||||||
Authors | Flood, R.J. / Ramberg, K. / Guagnini, F. / Crowley, P.B. | ||||||||||||
Funding support | Ireland, 3items
| ||||||||||||
Citation | Journal: Cryst.Growth Des. / Year: 2022 Title: Protein Frameworks with Thiacalixarene and Zinc. Authors: Flood, R.J. / Ramberg, K.O. / Mengel, D.B. / Guagnini, F. / Crowley, P.B. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7pr4.cif.gz | 68 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7pr4.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 7pr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/7pr4 ftp://data.pdbj.org/pub/pdb/validation_reports/pr/7pr4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7pr2C 7pr3C 7pr5C 5lycS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#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 |
---|
-Non-polymers , 5 types, 164 molecules
#2: Chemical | ChemComp-HEC / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-80M / | ||||
#4: Chemical | ChemComp-ZN / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.05 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% PEG 3350, 100 mM sodium acetate pH 5.6, 10 mM zinc acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→41.45 Å / Num. obs: 26001 / % possible obs: 99.6 % / Redundancy: 10.6 % / CC1/2: 0.984 / Rpim(I) all: 0.065 / Rrim(I) all: 0.217 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.3→1.3 Å / Num. unique obs: 1216 / CC1/2: 0.798 / Rpim(I) all: 0.418 / Rrim(I) all: 0.881 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LYC Resolution: 1.32→41.45 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.12 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.39 Å2 / Biso mean: 16.2965 Å2 / Biso min: 7.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.32→41.45 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
|