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Open data
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Basic information
Entry | Database: PDB / ID: 8pu4 | ||||||
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Title | FaRel2 bound to the ATP analogue, APCPP | ||||||
![]() | RelA/SpoT domain-containing protein | ||||||
![]() | ANTITOXIN / Toxin / toxSAS / RSH / small alormone synthetase / phage defence | ||||||
Function / homology | guanosine tetraphosphate biosynthetic process / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / Nucleotidyltransferase superfamily / : / RelA/SpoT domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Garcia-Pino, A. / Talavera Perez, A. / Dominguez Molina, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: FaRel2 bound to the ATP analogue, APCPP Authors: Garcia-Pino, A. / Talavera Perez, A. / Dominguez Molina, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227.6 KB | Display | ![]() |
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PDB format | ![]() | 173.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24726.076 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | Mass: 505.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 12 % w/v PEG 2000, 50 mM MES pH 5.5 |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→59.1 Å / Num. obs: 16326 / % possible obs: 90.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 51.19 Å2 / CC1/2: 0.985 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.62→2.83 Å / Num. unique obs: 818 / CC1/2: 0.332 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 53.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.62→59.05 Å
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Refine LS restraints |
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LS refinement shell |
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