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Yorodumi- PDB-6d0i: ParT: Prs ADP-ribosylating toxin bound to cognate antitoxin ParS.... -
+Open data
-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. | ||||||
Components |
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Keywords | TOXIN / ADP-ribosyltransferase / toxin-antitoxin complex / ParST | ||||||
Function / homology | Function and homology information glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / DNA binding Similarity search - Function | ||||||
Biological species | Sphingobium sp. YBL2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å | ||||||
Model details | SeMet-substituted L48M toxin in complex with C-terminal antitoxin fragment | ||||||
Authors | Piscotta, F.J. / Jeffrey, P.D. / Link, A.J. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d0i.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d0i.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 6d0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/6d0i ftp://data.pdbj.org/pub/pdb/validation_reports/d0/6d0i | HTTPS FTP |
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-Related structure data
-Links
-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.) Sphingobium sp. YBL2 (bacteria) / Gene: TZ53_17660 / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0C5XL88 #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.) Sphingobium sp. YBL2 (bacteria) / Gene: TZ53_17665 / Plasmid: pRSFduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0C5XKJ0 #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979272 Å | ||||||||||||||||||||||||
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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