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- PDB-6sd6: Structure of VapBC from Shigella sonnei -

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Basic information

Entry
Database: PDB / ID: 6sd6
TitleStructure of VapBC from Shigella sonnei
Components
  • Antitoxin
  • tRNA(fMet)-specific endonuclease VapC
KeywordsTOXIN / VapBC Toxin-antitoxin complex
Function / homology
Function and homology information


RNA nuclease activity / toxin activity / Hydrolases; Acting on ester bonds / magnesium ion binding / DNA binding
Similarity search - Function
: / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / PIN domain / SpoVT-AbrB domain superfamily / VapC family / PIN domain / PIN-like domain superfamily
Similarity search - Domain/homology
tRNA(fMet)-specific endonuclease VapC / Antitoxin
Similarity search - Component
Biological speciesShigella sonnei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsLea, S.M. / Hollingshead, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust102908/Z/13/Z United Kingdom
CitationJournal: To Be Published
Title: Polymorphisms in the VapBC toxin:antitoxin system mediate high frequency plasmid loss in Shigella sonnei
Authors: Martyn, J.E. / Pilla, G. / Hollingshead, S. / Lea, S.M. / McVicker, G. / Tang, C.M.
History
DepositionJul 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Antitoxin
B: Antitoxin
C: tRNA(fMet)-specific endonuclease VapC
D: tRNA(fMet)-specific endonuclease VapC


Theoretical massNumber of molelcules
Total (without water)51,1624
Polymers51,1624
Non-polymers00
Water48627
1
A: Antitoxin
B: Antitoxin
C: tRNA(fMet)-specific endonuclease VapC
D: tRNA(fMet)-specific endonuclease VapC

A: Antitoxin
B: Antitoxin
C: tRNA(fMet)-specific endonuclease VapC
D: tRNA(fMet)-specific endonuclease VapC


Theoretical massNumber of molelcules
Total (without water)102,3248
Polymers102,3248
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area25200 Å2
ΔGint-94 kcal/mol
Surface area35350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.873, 95.873, 116.389
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Antitoxin / VapB


Mass: 8545.569 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella sonnei (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3U1ZEK5
#2: Protein tRNA(fMet)-specific endonuclease VapC / RNase VapC / Toxin VapC


Mass: 17035.455 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella sonnei (bacteria) / Gene: vapC, BZ172_30265 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0H9P9N5, Hydrolases; Acting on ester bonds
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.41 Å3/Da / Density % sol: 63.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Ammonium sulphate 0.3 M sodium formate 0.1 M sodium cacodylate pH 6.5 3% w/v PGA and 5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.61→83 Å / Num. obs: 19316 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 71.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.043 / Rrim(I) all: 0.134 / Net I/σ(I): 9.4
Reflection shellResolution: 2.61→2.65 Å / Rmerge(I) obs: 2.665 / Mean I/σ(I) obs: 1 / Num. unique obs: 922 / CC1/2: 0.502 / Rpim(I) all: 0.919

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Processing

Software
NameVersionClassification
PHENIXdev_3523refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TND

3tnd


Resolution: 2.61→35.15 Å / SU ML: 0.4114 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.4172
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.236 931 4.87 %
Rwork0.2064 18184 -
obs0.2078 19115 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.58 Å2
Refinement stepCycle: LAST / Resolution: 2.61→35.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 0 27 3191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00173217
X-RAY DIFFRACTIONf_angle_d0.44884343
X-RAY DIFFRACTIONf_chiral_restr0.0412486
X-RAY DIFFRACTIONf_plane_restr0.0032571
X-RAY DIFFRACTIONf_dihedral_angle_d12.36211959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.750.40541280.3472524X-RAY DIFFRACTION97.46
2.75-2.920.35621230.32222557X-RAY DIFFRACTION99.08
2.92-3.140.3411360.28252557X-RAY DIFFRACTION99.15
3.14-3.460.3251390.25492559X-RAY DIFFRACTION99.23
3.46-3.960.24321200.21182628X-RAY DIFFRACTION99.28
3.96-4.990.22311330.16952635X-RAY DIFFRACTION99.86
4.99-35.150.17361520.16962724X-RAY DIFFRACTION99.38

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