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- PDB-6d0h: ParT: Prs ADP-ribosylating toxin bound to cognate antitoxin ParS -

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Basic information

Entry
Database: PDB / ID: 6d0h
TitleParT: Prs ADP-ribosylating toxin bound to cognate antitoxin ParS
Components
  • ParS: COG5642 (DUF2384) antitoxin
  • 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 / Resolution: 1.5 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 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,9936
Polymers49,8084
Non-polymers1842
Water13,367742
1
A: ParT: COG5654 (RES domain) toxin
B: ParS: COG5642 (DUF2384) antitoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9963
Polymers24,9042
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-15 kcal/mol
Surface area10970 Å2
MethodPISA
2
C: ParT: COG5654 (RES domain) toxin
D: ParS: COG5642 (DUF2384) antitoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9963
Polymers24,9042
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-12 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.867, 51.342, 57.797
Angle α, β, γ (deg.)84.310, 73.930, 84.780
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 17291.643 Da / Num. of mol.: 2 / Fragment: RES domain
Source method: isolated from a genetically manipulated source
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


Mass: 7612.536 Da / Num. of mol.: 2 / Fragment: DUF2384
Source method: isolated from a genetically manipulated source
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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 742 / Source method: isolated from a natural source / Formula: H2O

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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: 48.31 % / Mosaicity: 0.815 °
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R 300K / Detector: PIXEL / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→40 Å / Num. obs: 76745 / % possible obs: 94.1 % / Redundancy: 2.9 % / Biso Wilson estimate: 10.35 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.029 / Rrim(I) all: 0.057 / Χ2: 1.32 / Net I/σ(I): 19.3 / Num. measured all: 220685
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.481.20.20219650.8780.1960.2820.94348.1
1.48-1.51.30.17529700.9120.1670.2420.92872.4
1.5-1.531.50.15537370.9240.1480.2140.92692.6
1.53-1.561.60.13138230.9520.1230.180.84293.6
1.56-1.61.60.11238630.9670.1050.1540.80394.6
1.6-1.631.70.10538610.9670.0980.1440.84595.7
1.63-1.671.80.09639680.9750.0850.1291.1196.5
1.67-1.7220.10239360.9740.0830.1331.60497.1
1.72-1.772.30.10840080.9690.0830.1371.81597.8
1.77-1.832.60.10440190.9760.0740.1291.87898.6
1.83-1.8930.140240.9780.0670.1211.7698.8
1.89-1.973.50.09940470.9790.0610.1171.97699.1
1.97-2.0640.08940620.9870.0520.1031.90599.7
2.06-2.1740.06940440.9920.0390.0791.46699.7
2.17-2.340.05940770.9850.0340.0681.20899.6
2.3-2.484.10.04740580.9960.0270.0540.92599.8
2.48-2.734.10.04440720.9940.0250.050.91199.9
2.73-3.1240.04140730.9970.0230.0470.941100
3.12-3.9340.03940860.9970.0220.0451.22699.9
3.93-403.70.03240520.9980.0190.0381.00799.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
MERLOTphasing
RefinementResolution: 1.5→24.625 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 16.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.175 3521 5.02 %
Rwork0.1476 66580 -
obs0.149 70101 95.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.71 Å2 / Biso mean: 16.129 Å2 / Biso min: 4.01 Å2
Refinement stepCycle: final / Resolution: 1.5→24.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 12 742 4244
Biso mean--17.37 28.27 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063659
X-RAY DIFFRACTIONf_angle_d1.15013
X-RAY DIFFRACTIONf_chiral_restr0.041579
X-RAY DIFFRACTIONf_plane_restr0.006652
X-RAY DIFFRACTIONf_dihedral_angle_d10.9171349
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.52050.21451390.17162379251887
1.5205-1.54230.20911280.16712461258988
1.5423-1.56530.18031270.15822502262989
1.5653-1.58970.20071400.15422478261890
1.5897-1.61580.16731370.15222584272191
1.6158-1.64370.18721250.14862554267992
1.6437-1.67350.17711320.14932607273993
1.6735-1.70570.17991370.14842656279393
1.7057-1.74050.19591290.15472552268194
1.7405-1.77840.20541320.15612641277395
1.7784-1.81970.18561440.15712716286095
1.8197-1.86520.19381550.1512648280396
1.8652-1.91560.20331460.14952677282396
1.9156-1.9720.19281450.15262703284897
1.972-2.03560.21551470.15492750289799
2.0356-2.10830.17281340.14472763289799
2.1083-2.19270.15111490.14012777292699
2.1927-2.29240.15991370.14442782291999
2.2924-2.41320.18151350.14822741287698
2.4132-2.56420.1731470.15442783293099
2.5642-2.76190.18441490.15382743289299
2.7619-3.03940.17391510.15072765291698
3.0394-3.47820.16241700.14072748291899
3.4782-4.37810.1461450.125327882933100
4.3781-24.62820.16161410.151827822923100

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