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- PDB-6d0i: ParT: Prs ADP-ribosylating toxin bound to cognate antitoxin ParS.... -

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Basic information

Entry
Database: PDB / ID: 6d0i
TitleParT: Prs ADP-ribosylating toxin bound to cognate antitoxin ParS. L48M ParT, SeMet-substituted complex.
Components
  • ParS: COG5642 (DUF2384) antitoxin fragment
  • ParT: COG5654 (RES domain) toxin
KeywordsTOXIN / ADP-ribosyltransferase / toxin-antitoxin complex / ParST
Function / homology
Function and homology information


glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / DNA binding
Similarity search - Function
Antitoxin Xre-like, helix-turn-helix domain / Antitoxin Xre-like helix-turn-helix domain / Antitoxin Xre/MbcA/ParS-like, toxin-binding domain / Antitoxin Xre/MbcA/ParS C-terminal toxin-binding domain / RES domain / RES domain / RES
Similarity search - Domain/homology
Prs ADP-ribosylating antitoxin / Prs ADP-ribosylating toxin
Similarity search - Component
Biological speciesSphingobium sp. YBL2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
Model detailsSeMet-substituted L48M toxin in complex with C-terminal antitoxin fragment
AuthorsPiscotta, F.J. / Jeffrey, P.D. / Link, A.J.
CitationJournal: 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
DepositionApr 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ParT: COG5654 (RES domain) toxin
B: ParS: COG5642 (DUF2384) antitoxin fragment
C: ParT: COG5654 (RES domain) toxin
D: ParS: COG5642 (DUF2384) antitoxin fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3125
Polymers50,2204
Non-polymers921
Water9,800544
1
A: ParT: COG5654 (RES domain) toxin
B: ParS: COG5642 (DUF2384) antitoxin fragment


Theoretical massNumber of molelcules
Total (without water)25,1102
Polymers25,1102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-14 kcal/mol
Surface area10830 Å2
MethodPISA
2
C: ParT: COG5654 (RES domain) toxin
D: ParS: COG5642 (DUF2384) antitoxin fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2023
Polymers25,1102
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-10 kcal/mol
Surface area10300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.977, 51.319, 57.941
Angle α, β, γ (deg.)84.680, 73.820, 85.510
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ParT: COG5654 (RES domain) toxin


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 ParS: COG5642 (DUF2384) antitoxin fragment


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 / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.32 % / Mosaicity: 0.09 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 10% MPD, 100 mM sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979272 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979272 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.51-1.558.30.68241790.7890.2490.72877.8
6.74-29.0310.20.0978020.9920.0320.10398.6

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
MERLOTphasing
RefinementResolution: 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
RfactorNum. reflection% reflection
Rfree0.1903 3235 4.99 %
Rwork0.1588 61583 -
obs0.1604 64818 96.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.37 Å2 / Biso mean: 19.8399 Å2 / Biso min: 6.77 Å2
Refinement stepCycle: final / Resolution: 1.55→29.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 6 544 4034
Biso mean--20.49 31.25 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063645
X-RAY DIFFRACTIONf_angle_d1.1124995
X-RAY DIFFRACTIONf_chiral_restr0.042577
X-RAY DIFFRACTIONf_plane_restr0.006650
X-RAY DIFFRACTIONf_dihedral_angle_d10.5391342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.57320.28031310.24552600273194
1.5732-1.59770.26331530.24172600275394
1.5977-1.62390.24331250.22422607273295
1.6239-1.65190.26031320.20712623275594
1.6519-1.6820.22351480.18922655280396
1.682-1.71430.19051260.18662659278595
1.7143-1.74930.22541290.1832674280396
1.7493-1.78730.24611330.18072640277396
1.7873-1.82890.21171510.16052668281996
1.8289-1.87460.18271460.14972619276596
1.8746-1.92530.18471440.15112704284897
1.9253-1.98190.21521510.16082654280597
1.9819-2.04590.22821360.1562671280797
2.0459-2.1190.20421370.1552721285897
2.119-2.20380.17191320.15092703283597
2.2038-2.30410.18661420.15612700284298
2.3041-2.42550.18541360.15622697283398
2.4255-2.57740.17661370.15622708284598
2.5774-2.77620.2031510.15772738288998
2.7762-3.05530.19251430.15722728287199
3.0553-3.49680.15611700.14472710288099
3.4968-4.40320.1611410.13042738287999
4.4032-29.03460.17771410.161627662907100

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