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- PDB-8zvb: The ShosTA toxin-antitoxin system provides phage defence -

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Basic information

Entry
Database: PDB / ID: 8zvb
TitleThe ShosTA toxin-antitoxin system provides phage defence
ComponentsShosT
KeywordsIMMUNE SYSTEM / ShosT / toxin
Function / homologyPhosphoribosyltransferase-like / Phosphoribosyltransferase domain / HAD superfamily / HAD-like superfamily / metal ion binding / Uncharacterized protein
Function and homology information
Biological speciesEscherichia coli O1:K1 / APEC (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsYu, Y. / Chen, Q.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: Nat Commun / Year: 2025
Title: A toxin-antitoxin system provides phage defense via DNA damage and repair.
Authors: Pu, H. / Chen, Y. / Zhao, X. / Dai, L. / Tong, A. / Tang, D. / Chen, Q. / Yu, Y.
History
DepositionJun 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ShosT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2243
Polymers49,0971
Non-polymers1282
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.381, 64.736, 64.473
Angle α, β, γ (deg.)90.000, 91.123, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein ShosT


Mass: 49096.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O1:K1 / APEC (bacteria)
Gene: APECO1_1183 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2Z117
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.15 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 20%PEG 6000, 0.1M MES pH6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 25046 / % possible obs: 98.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 23.73 Å2 / CC1/2: 0.966 / Net I/σ(I): 8.7
Reflection shellResolution: 2.09→2.12 Å / Num. unique obs: 1195 / CC1/2: 0.802

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→39.57 Å / SU ML: 0.2445 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.5765
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2236 934 4.13 %
Rwork0.1922 21660 -
obs0.1936 22594 87.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.17 Å2
Refinement stepCycle: LAST / Resolution: 2.04→39.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 7 147 3329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673269
X-RAY DIFFRACTIONf_angle_d0.58984437
X-RAY DIFFRACTIONf_chiral_restr0.0486490
X-RAY DIFFRACTIONf_plane_restr0.0041566
X-RAY DIFFRACTIONf_dihedral_angle_d4.4072699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.150.3003550.22281745X-RAY DIFFRACTION48.67
2.15-2.290.2428930.21932741X-RAY DIFFRACTION77.52
2.29-2.460.27681320.21573330X-RAY DIFFRACTION93.9
2.46-2.710.29381470.21233483X-RAY DIFFRACTION98.45
2.71-3.10.23991700.20563475X-RAY DIFFRACTION98.86
3.1-3.910.21561750.18423444X-RAY DIFFRACTION97.78
3.91-39.570.17891620.16663442X-RAY DIFFRACTION95.29

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