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- PDB-9h6b: Crystal structure of the E. coli F-plasmid VapBC toxin-antitoxin ... -

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Basic information

Entry
Database: PDB / ID: 9h6b
TitleCrystal structure of the E. coli F-plasmid VapBC toxin-antitoxin complex (VapB T3N, A13P, L16R)
Components
  • Antitoxin
  • tRNA(fMet)-specific endonuclease VapC
KeywordsTOXIN / VapBC / toxin-antitoxin / antibiotic tolerance
Function / homology
Function and homology information


RNA nuclease activity / toxin activity / endonuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding / DNA binding
Similarity search - Function
: / : / : / 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
Toxin-antitoxin system antitoxin VapB / tRNA(fMet)-specific endonuclease VapC
Similarity search - Component
Biological speciesEscherichia coli KLY (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHollingshead, S. / McVicker, G. / Nielsen, M.R. / Zhang, Y. / Pilla, G. / Jones, R.A. / Thomas, J.C. / Johansen, S.E.H. / Exley, R.M. / Brodersen, D.E. / Tang, C.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust221924/Z/20/Z United Kingdom
CitationJournal: Mbio / Year: 2025
Title: Shared mechanisms of enhanced plasmid maintenance and antibiotic tolerance mediated by the VapBC toxin:antitoxin system.
Authors: Hollingshead, S. / McVicker, G. / Nielsen, M.R. / Zhang, Y. / Pilla, G. / Jones, R.A. / Thomas, J.C. / Johansen, S.E.H. / Exley, R.M. / Brodersen, D.E. / Tang, C.M.
History
DepositionOct 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 12, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,6704
Polymers51,6704
Non-polymers00
Water00
1
A: tRNA(fMet)-specific endonuclease VapC
B: Antitoxin
C: tRNA(fMet)-specific endonuclease VapC
D: Antitoxin

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


Theoretical massNumber of molelcules
Total (without water)103,3418
Polymers103,3418
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area26770 Å2
ΔGint-84 kcal/mol
Surface area32990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.590, 89.590, 115.978
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
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 tRNA(fMet)-specific endonuclease VapC / RNase VapC / Toxin VapC


Mass: 14818.081 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli KLY (bacteria)
Gene: orf5, vapC, EWK56_24100, F7N46_24920, FGAF1022_52400, FGAS143_47190, G4A38_21190, G4A47_21040
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q84A22, Hydrolases; Acting on ester bonds
#2: Protein Antitoxin / VapB protein (Antitoxin to VapC)


Mass: 11017.136 Da / Num. of mol.: 2 / Mutation: T3N, A13P, L16R
Source method: isolated from a genetically manipulated source
Details: T3N, A13P, L16R mutant / Source: (gene. exp.) Escherichia coli KLY (bacteria)
Gene: orf6, vapB, ACN81_23035, FGAF1022_52390, FGAS143_47180, G4A38_21185, G4A47_21035
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7B3V0
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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M Lithium sulphate monohydrate, 0.1 M sodium citrate tribasic dihydrate, 26 % PEG200
PH range: 5.0-5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.979261 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979261 Å / Relative weight: 1
ReflectionResolution: 2.8→46.5 Å / Num. obs: 13688 / % possible obs: 99.9 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.098 / Net I/σ(I): 14.13
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.8-2.872.8069930.3332.9561
2.87-2.952.1369440.5032.2481
2.95-3.041.6549640.621.7411
3.04-3.131.1839140.7841.2441
3.13-3.230.8128960.8660.8551
3.23-3.350.5668490.9250.5961
3.35-3.470.4298290.960.4511
3.47-3.620.2838180.9830.2981
3.62-3.780.1897690.9940.1991
3.78-3.960.1447390.9940.1521
3.96-4.180.1067080.9970.1111
4.18-4.430.0886750.9970.0931
4.43-4.740.076400.9980.0741
4.74-5.110.0625710.9990.0661
5.11-5.60.0655640.9980.0681
5.6-6.260.0664940.9980.071
6.26-7.230.0514440.9990.0541
7.23-8.860.0433870.9990.0451
8.86-12.530.0373020.9990.041
12.53-46.50.0361880.9980.0381

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(1.21.1_5286: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→46.45 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 1374 10.05 %
Rwork0.2301 --
obs0.2346 13673 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 0 0 3175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063229
X-RAY DIFFRACTIONf_angle_d0.9074361
X-RAY DIFFRACTIONf_dihedral_angle_d20.0981221
X-RAY DIFFRACTIONf_chiral_restr0.057485
X-RAY DIFFRACTIONf_plane_restr0.01577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90.5181350.50031198X-RAY DIFFRACTION99
2.9-3.020.50531340.41691194X-RAY DIFFRACTION100
3.02-3.150.37571330.34231213X-RAY DIFFRACTION100
3.16-3.320.3011370.29491227X-RAY DIFFRACTION100
3.32-3.530.32711370.29451214X-RAY DIFFRACTION100
3.53-3.80.30691400.2631205X-RAY DIFFRACTION100
3.8-4.180.27591360.21831234X-RAY DIFFRACTION100
4.18-4.790.22981340.19811237X-RAY DIFFRACTION100
4.79-6.030.3091380.2181262X-RAY DIFFRACTION100
6.03-46.450.22261500.18961315X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.0542-0.59-3.31614.8332-5.4048.47220.04640.40650.7983-0.1690.36890.874-2.2614-0.6859-0.56951.36840.0529-0.09040.77180.07940.746230.001715.7257-2.5933
23.46091.246-0.17068.79380.85648.46920.0843-0.0204-0.56740.1750.2028-0.9684-0.4710.4647-0.25060.8903-0.0038-0.01280.7465-0.04630.794737.108611.083518.2931
35.5826-0.89721.88624.17543.12778.081-0.2052-0.25440.1753-0.31560.4138-0.4329-0.08320.5033-0.30920.9033-0.11810.02860.7103-0.04910.787341.22326.343111.3954
42.0197-6.43011.4247.985-2.01942.4687-1.9374-2.6385-4.1385-0.19772.46564.9072.3181-1.3332-1.32451.32590.21270.49941.7790.33411.99378.526-12.76956.4077
50.4937-0.8174-0.74452.55132.80033.174-0.96490.92292.3082-2.86363.15422.1013-1.203-4.333-1.3511.7882-0.136-0.43792.70270.81012.3504-0.4806-7.6872-5.6734
60.9596-1.81972.01341.97522.01517.5845-1.26811.60070.1548-6.4341-0.35372.26072.2181-2.5098-3.82781.48820.2229-0.85771.32760.25991.92251.5991-7.6928-8.9302
78.1021-3.4504-6.28032.43813.12385.137-0.59371.9311-0.60090.71580.2676-0.3399-2.0131-2.50360.81051.52460.30880.2161.88240.0371.4989.3919-5.52085.1587
87.16743.3639-2.20266.1401-3.55696.2055-0.27320.16560.3870.60870.12491.1024-0.78720.27670.73831.02380.0544-0.14571.22110.09471.107215.4034-6.6828-5.764
95.5031-4.5487-3.09975.43880.48524.2709-0.16281.453-0.4366-3.50681.5792-0.1033-0.9149-0.4155-0.9432.0793-0.4277-0.08210.9994-0.09941.288632.58957.8399-9.8883
102.08660.37892.28270.03710.11530.48661.3465.1091-1.0211.23841.6457-0.0195-2.16484.86780.08781.7163-0.2472-0.10651.4662-0.23951.096341.467921.92124.274
114.45091.99890.2436.4489-0.26941.6736-0.79110.49570.5303-0.18930.1799-0.0603-0.8511-0.04750.5581.1857-0.0577-0.0340.8136-0.07450.734723.642926.263425.8551
122.1188-0.8255-0.89366.3121.90978.71110.13530.29510.0658-0.3267-0.40860.6003-0.3088-0.53330.01170.82770.0911-0.11850.5095-0.02750.705325.722720.685724.4903
138.4037-2.4178-0.19685.20031.49147.311-0.15511.75810.6655-1.654-0.4196-0.446-1.3938-0.25760.22831.36640.0222-0.15340.8079-0.0980.8926.683827.219911.6732
145.0403-1.06630.45392.0775-2.87094.1962-0.23641.3556-2.5927-2.7184-0.08550.9646-0.10062.73110.22052.39940.1242-0.40621.3707-0.25870.828729.706535.470319.2699
155.0167-1.36391.75872.0729-1.3485.025-1.6664-0.63212.4296-1.10931.88730.76950.28891.70420.35852.18420.4516-0.49911.1098-0.14411.125222.307433.924216.7362
164.3832-4.24365.39524.7587-4.098.05593.2886-1.8014-0.3244-1.3377-2.0286-2.0678-0.0587-1.1115-0.73641.8934-0.34690.47552.05890.55721.490513.56314.61752.2371
172.98340.48431.55225.8179-4.01015.3231-0.4409-0.2146-1.94952.40621.29690.96350.1366-2.12541.26231.2275-0.1260.66831.59110.18882.23414.2924-0.074439.6911
185.5338-0.3271-3.55991.8653-0.51392.6473-0.38572.5633-2.5439-0.81813.3037-1.05651.35844.1076-2.61671.2608-0.13830.1391.3601-0.65611.36946.29470.828237.3499
194.98852.4068-3.46652.9187-1.54043.71362.5223-2.32511.6232-0.628-1.65231.52720.67270.252-0.51621.86460.39160.17111.233-0.33062.35736.97559.276550.9709
205.98970.2303-2.54963.0989-0.82845.47430.1064-0.1885-0.20670.3834-0.01880.2228-0.23610.1457-0.04650.82290.0686-0.02290.8677-0.1430.828920.967119.647736.1398
216.94993.85931.03986.73410.37514.6226-0.39920.5197-0.7668-1.08710.2228-0.72110.6465-0.07510.00020.8286-0.11330.08570.9021-0.06570.650736.91162.2668-0.9125
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 34 through 66 )
2X-RAY DIFFRACTION2chain 'C' and (resid 67 through 95 )
3X-RAY DIFFRACTION3chain 'C' and (resid 96 through 132 )
4X-RAY DIFFRACTION4chain 'D' and (resid 0 through 4 )
5X-RAY DIFFRACTION5chain 'D' and (resid 5 through 9 )
6X-RAY DIFFRACTION6chain 'D' and (resid 10 through 14 )
7X-RAY DIFFRACTION7chain 'D' and (resid 15 through 20 )
8X-RAY DIFFRACTION8chain 'D' and (resid 21 through 42 )
9X-RAY DIFFRACTION9chain 'D' and (resid 43 through 61 )
10X-RAY DIFFRACTION10chain 'D' and (resid 62 through 68 )
11X-RAY DIFFRACTION11chain 'A' and (resid 1 through 17 )
12X-RAY DIFFRACTION12chain 'A' and (resid 18 through 87 )
13X-RAY DIFFRACTION13chain 'A' and (resid 88 through 114 )
14X-RAY DIFFRACTION14chain 'A' and (resid 115 through 119 )
15X-RAY DIFFRACTION15chain 'A' and (resid 120 through 132 )
16X-RAY DIFFRACTION16chain 'B' and (resid 0 through 4 )
17X-RAY DIFFRACTION17chain 'B' and (resid 5 through 9 )
18X-RAY DIFFRACTION18chain 'B' and (resid 10 through 14 )
19X-RAY DIFFRACTION19chain 'B' and (resid 15 through 20 )
20X-RAY DIFFRACTION20chain 'B' and (resid 21 through 69 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1 through 33 )

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