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- PDB-8zva: structure of ShosA from E.coli APEC O1 -

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Basic information

Entry
Database: PDB / ID: 8zva
Titlestructure of ShosA from E.coli APEC O1
ComponentsDNA processing protein DprA
KeywordsIMMUNE SYSTEM / DprA / antitoxin / ShosA
Function / homologyDNA recombination-mediator protein A / DNA recombination-mediator protein A / DNA-mediated transformation / DNA processing protein DprA
Function and homology information
Biological speciesEscherichia coli O1:K1 / APEC (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYu, Y. / Chen, Q. / Pu, H.
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: DNA processing protein DprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4334
Polymers35,2131
Non-polymers2203
Water99155
1
A: DNA processing protein DprA
hetero molecules

A: DNA processing protein DprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8658
Polymers70,4262
Non-polymers4396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4040 Å2
ΔGint-57 kcal/mol
Surface area27270 Å2
MethodPISA
2
A: DNA processing protein DprA
hetero molecules

A: DNA processing protein DprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8658
Polymers70,4262
Non-polymers4396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4450 Å2
ΔGint-40 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.029, 70.029, 120.323
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-553-

HOH

21A-555-

HOH

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Components

#1: Protein DNA processing protein DprA / ShosA


Mass: 35212.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O1:K1 / APEC (bacteria)
Gene: APECO1_1182 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2Z0G0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / 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.: 55 / 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: 2.09 Å3/Da / Density % sol: 41.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 2000,0.1M imidazole pH 7.0, 0.2M Ammonia citrate pH7.0

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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: Oct 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 24225 / % possible obs: 94.7 % / Redundancy: 20 % / Biso Wilson estimate: 30.73 Å2 / CC1/2: 1 / Net I/σ(I): 21
Reflection shellResolution: 1.9→2.02 Å / Num. unique obs: 3239 / CC1/2: 0.945

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→49.52 Å / SU ML: 0.3945 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.767
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2724 1111 5 %
Rwork0.2466 21117 -
obs0.2479 22228 91.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.27 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 13 55 2491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00492494
X-RAY DIFFRACTIONf_angle_d0.61673390
X-RAY DIFFRACTIONf_chiral_restr0.0444383
X-RAY DIFFRACTIONf_plane_restr0.0034430
X-RAY DIFFRACTIONf_dihedral_angle_d2.86532048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.990.6419980.64191828X-RAY DIFFRACTION65.22
1.99-2.090.43531450.38822781X-RAY DIFFRACTION98.92
2.09-2.220.34441450.31962795X-RAY DIFFRACTION98.36
2.22-2.40.34551060.30512022X-RAY DIFFRACTION71.19
2.4-2.640.30021500.2442847X-RAY DIFFRACTION99.3
2.64-3.020.31021520.24512867X-RAY DIFFRACTION99.64
3.02-3.80.28451520.24142893X-RAY DIFFRACTION99.22
3.8-49.520.19791630.19463084X-RAY DIFFRACTION99.75

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