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- PDB-7pr3: Cocrystal Form I of a cytochrome c, sulfonato-thiacalix[4]arene -... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pr3 | ||||||||||||
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Title | Cocrystal Form I of a cytochrome c, sulfonato-thiacalix[4]arene - zinc cluster | ||||||||||||
![]() | Cytochrome c iso-1 | ||||||||||||
![]() | ELECTRON TRANSPORT / calixarene / molecular glue / synthetic receptor / alpha helix / thiacalixarene / metal cluster | ||||||||||||
Function / homology | ![]() Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / mitochondrial intermembrane space / electron transfer activity / heme binding ...Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / 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 | ![]()
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![]() | ![]() Title: Protein Frameworks with Thiacalixarene and Zinc. Authors: Flood, R.J. / Ramberg, K.O. / Mengel, D.B. / Guagnini, F. / Crowley, P.B. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.6 KB | Display | ![]() |
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PDB format | ![]() | 91.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.2 MB | Display | ![]() |
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Full document | ![]() | 5.2 MB | Display | |
Data in XML | ![]() | 20.1 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pr2C ![]() 7pr4C ![]() 7pr5C ![]() 5lycS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 12041.770 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CYC1, YJR048W, J1653 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 121 molecules ![](data/chem/img/HEC.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/80M.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/80M.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-80M / #5: Chemical | ChemComp-PO4 / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% PEG 3350, 100 mM sodium acetate pH 5.6, 30 mM zinc acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: 2.4→63.5 Å / Num. obs: 21540 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.996 / Rpim(I) all: 0.1 / Rrim(I) all: 0.363 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.4→2.4 Å / Num. unique obs: 1057 / CC1/2: 0.791 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LYC Resolution: 2.37→63.55 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.57 / 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: 106.1 Å2 / Biso mean: 36.9177 Å2 / Biso min: 24.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.37→63.55 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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