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- PDB-6d0i: ParT: Prs ADP-ribosylating toxin bound to cognate antitoxin ParS.... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d0i | ||||||
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Title | ParT: Prs ADP-ribosylating toxin bound to cognate antitoxin ParS. L48M ParT, SeMet-substituted complex. | ||||||
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![]() | TOXIN / ADP-ribosyltransferase / toxin-antitoxin complex / ParST | ||||||
Function / homology | ![]() glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
Model details | SeMet-substituted L48M toxin in complex with C-terminal antitoxin fragment | ||||||
![]() | Piscotta, F.J. / Jeffrey, P.D. / Link, A.J. | ||||||
![]() | ![]() Title: ParST is a widespread toxin-antitoxin module that targets nucleotide metabolism. Authors: Piscotta, F.J. / Jeffrey, P.D. / Link, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.9 KB | Display | ![]() |
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PDB format | ![]() | 88.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.2 KB | Display | ![]() |
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Full document | ![]() | 459.7 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17403.471 Da / Num. of mol.: 2 / Fragment: RES domain / Mutation: L48M Source method: isolated from a genetically manipulated source Details: SeMet-substituted / Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 7706.326 Da / Num. of mol.: 2 / Fragment: DUF2384 Source method: isolated from a genetically manipulated source Details: SeMet-substituted / Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.32 % / Mosaicity: 0.09 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 10% MPD, 100 mM sodium acetate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 20, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979272 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.51→29.03 Å / Num. obs: 69683 / % possible obs: 95.5 % / Redundancy: 10.5 % / Biso Wilson estimate: 14.29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.037 / Rrim(I) all: 0.122 / Net I/σ(I): 13.6 / Num. measured all: 731885 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Resolution: 1.55→29.03 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 19.67 / 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: 84.37 Å2 / Biso mean: 19.8399 Å2 / Biso min: 6.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→29.03 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23
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