+
Open data
-
Basic information
Entry | Database: PDB / ID: 7pr2 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cocrystal of cytochrome c and sulfonato-thiacalix[4]arene | ||||||||||||
![]() | Cytochrome c iso-1 | ||||||||||||
![]() | ELECTRON TRANSPORT / calixarene / molecular glue / synthetic receptor / alpha helix / thiacalixarene | ||||||||||||
Function / homology | ![]() Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / mitochondrial intermembrane space / electron transfer activity ...Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / mitochondrial intermembrane space / electron transfer activity / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Flood, R.J. / Ramberg, K. / Guagnini, F. / Crowley, P.B. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() 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: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 69.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 50.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7pr3C ![]() 7pr4C ![]() 7pr5C ![]() 5lycS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 12041.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CYC1, YJR048W, J1653 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.3 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 25% PEG 3350, 100 mM tri-Sodium citrate pH 5.6, 100 mM Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 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: 1.7→52.2 Å / Num. obs: 23336 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.99 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.7→1.7 Å / Num. unique obs: 1143 / CC1/2: 0.79 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5lyc Resolution: 1.73→52.24 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.23 / 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: 71.5 Å2 / Biso mean: 25.3144 Å2 / Biso min: 12.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.73→52.24 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %
|