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- PDB-8zvd: ShosT with phosphate -

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Basic information

Entry
Database: PDB / ID: 8zvd
TitleShosT with phosphate
ComponentsShosT
KeywordsIMMUNE SYSTEM / ShooT / Toxin / Phosphoribosyltransferase / pyrophosphatase
Function / homologyPhosphoribosyltransferase-like / Phosphoribosyltransferase domain / HAD superfamily / HAD-like superfamily / metal ion binding / PHOSPHATE ION / Uncharacterized protein
Function and homology information
Biological speciesEscherichia coli O1:K1 / APEC (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsYu, Y. / Chen, Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
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)49,2873
Polymers49,0971
Non-polymers1902
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-8 kcal/mol
Surface area18260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.848, 64.288, 64.401
Angle α, β, γ (deg.)90.000, 90.578, 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.1 Å3/Da / Density % sol: 41.48 %
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: 289 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 43288 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.49 Å2 / CC1/2: 0.99 / Net I/σ(I): 18
Reflection shellResolution: 1.72→1.75 Å / Num. unique obs: 2123 / CC1/2: 0.838

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→28.79 Å / SU ML: 0.1654 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.926
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1936 1091 2.56 %
Rwork0.159 41478 -
obs0.1599 42569 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.44 Å2
Refinement stepCycle: LAST / Resolution: 1.72→28.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 10 339 3667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743427
X-RAY DIFFRACTIONf_angle_d0.78744656
X-RAY DIFFRACTIONf_chiral_restr0.0501512
X-RAY DIFFRACTIONf_plane_restr0.0048595
X-RAY DIFFRACTIONf_dihedral_angle_d4.20452828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.80.23871410.2094404X-RAY DIFFRACTION83.98
1.8-1.890.23011180.1825233X-RAY DIFFRACTION98.69
1.89-2.010.19171300.16765273X-RAY DIFFRACTION100
2.01-2.160.21521080.16225308X-RAY DIFFRACTION99.98
2.16-2.380.21651570.15595273X-RAY DIFFRACTION100
2.38-2.730.17861270.15345303X-RAY DIFFRACTION99.96
2.73-3.430.18121760.15245278X-RAY DIFFRACTION100
3.43-28.790.18291340.15325406X-RAY DIFFRACTION99.8

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