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- PDB-9h6d: Crystal structure of the E. coli F-plasmid VapBC toxin-antitoxin ... -

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Basic information

Entry
Database: PDB / ID: 9h6d
TitleCrystal structure of the E. coli F-plasmid VapBC toxin-antitoxin complex (VapB V5E)
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: 3.15 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)51,5644
Polymers51,5644
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)103,1298
Polymers103,1298
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area26260 Å2
ΔGint-114 kcal/mol
Surface area32370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.807, 89.807, 117.134
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: 10964.046 Da / Num. of mol.: 2 / Mutation: V5E
Source method: isolated from a genetically manipulated source
Details: V5E 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: 3.04 Å3/Da / Density % sol: 59.48 %
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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97702 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97702 Å / Relative weight: 1
ReflectionResolution: 3.15→46.8 Å / Num. obs: 9854 / % possible obs: 99.8 % / Redundancy: 20.08 % / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rrim(I) all: 0.123 / Net I/σ(I): 13.84
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.15-3.234.6927070.1674.9371
3.23-3.323.2816810.1313.4471
3.32-3.412.7276850.2942.8671
3.41-3.521.8926600.5621.9881
3.52-3.631.1216410.7571.1791
3.63-3.760.756290.9040.7891
3.76-3.90.5446030.9280.5731
3.9-4.060.3695710.970.3891
4.06-4.240.255620.9820.2641
4.24-4.450.1685290.9910.1781
4.45-4.690.1235100.9960.1291
4.69-4.980.1114850.9960.1171
4.98-5.320.1014500.9980.1071
5.32-5.750.1044310.9970.1091
5.75-6.290.0893930.9980.0931
6.29-7.040.0593640.9990.0631
7.04-8.130.043230.9990.0431
8.13-9.950.0272750.9990.0291
9.95-14.080.02322510.0241
14.08-46.80.02313010.0251

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(1.20.1_4487: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→46.79 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2984 527 5.39 %
Rwork0.2481 --
obs0.2509 9785 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 0 0 3166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053217
X-RAY DIFFRACTIONf_angle_d0.6794344
X-RAY DIFFRACTIONf_dihedral_angle_d4.554440
X-RAY DIFFRACTIONf_chiral_restr0.046487
X-RAY DIFFRACTIONf_plane_restr0.011573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.470.39241350.40852216X-RAY DIFFRACTION98
3.47-3.970.38971410.34472284X-RAY DIFFRACTION100
3.97-50.32121220.26862341X-RAY DIFFRACTION100
5-46.790.25551290.20172417X-RAY DIFFRACTION99
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)
17.4467-0.8758-0.34144.77966.28848.8318-0.19270.5653-0.27920.55060.0557-0.41450.51820.047-0.35891.41930.15090.01711.22990.34181.2217-23.8791-25.82226.3715
21.6921-0.9702-1.10076.2497-4.76629.3354-0.1347-2.717-1.02141.48060.5697-1.33263.55250.24510.41161.97980.226-0.15441.59870.02231.449-19.0206-29.419734.7185
35.651-0.7089-1.90853.21832.88863.46571.9951.21270.92530.4216-2.0979-1.96610.87141.70070.23871.42070.0491-0.02811.61320.61351.8454-13.0058-23.181827.2949
42.3866-4.868-0.27019.22671.83425.5544-0.48750.4689-0.65330.022-0.20250.07120.1603-0.8923-0.25191.20850.11890.10721.24740.14741.0541-32.2695-17.972224.4592
54.0165-1.20285.29353.918-2.52357.12540.8615-2.5061.20541.5912-0.91891.119-1.1576-1.1727-0.27521.34410.22770.13341.2714-0.10321.1983-30.9772-15.80334.8523
68.4646-1.71386.81524.46342.15468.71760.01621.8572-1.509-1.34551.5427-0.2743-5.76043.77220.78721.89450.18020.70221.16450.15991.6021-21.9952-15.481318.335
74.58010.9863-3.76869.71684.61295.39861.52311.7524-0.95771.615-1.3383-0.80630.7427-0.7259-0.35512.13530.17590.24481.7069-0.14151.3106-28.0008-25.51324.4118
88.69191.0321.00332.6387-1.26335.42830.96121.01491.2016-1.2801-1.01220.44430.82370.7959-0.23911.59840.13520.31171.3820.15081.7742-27.844-25.62512.0193
92.33081.1389-1.12648.35170.44853.0805-1.10781.3556-1.2388-3.26430.32920.22390.71010.2898-0.5961.85020.15250.24061.18390.11791.5629-25.5693-32.842317.7688
106.92035.0502-0.60973.5385-0.03334.4789-0.8931-1.0728-0.5532-1.34340.4837-2.13212.25352.76650.8071.88170.60480.69811.7874-0.08871.8988-20.385-32.918818.6101
112.00872.01242.0182.0182.00092.0019-0.98290.27315.4104-0.55925.2211-0.1612-7.05712.5058-0.43171.9735-0.5662-0.42152.13790.54891.8703-13.7358-3.298852.7757
125.6816-0.0985-0.7882.5908-1.26442.8453-0.3839-0.5644-1.55660.58771.63451.0897-0.01774.939-1.35772.6955-0.35281.12462.8307-0.23362.5484-5.23730.58940.3364
135.472-4.144-6.65543.33814.92248.16082.90072.38691.55242.5677-0.6368-1.1014-2.2155-3.1133-1.05271.4696-0.61190.06593.283-0.1422.0719-6.4005-0.972637.2035
142.0662-2.4258-9.44749.40082.69059.34512.9661-0.88750.9667-0.58092.15456.7949-2.5741-2.92542.71772.28891.0415-0.03283.04180.94192.0143-7.2088-8.284151.3386
157.3942-6.6313-0.36217.7013-1.93353.0749-3.4738-3.1375-0.49221.74454.07821.54240.6001-4.04330.29521.65980.12710.27772.780.1061.4657-3.2719-18.692144.5868
162.93193.71334.57489.27312.90568.3246-0.27321.55782.96960.8453-0.2866-1.3965-1.3191.2592-0.18551.27490.0873-0.01761.36440.01961.571-15.8283-11.403338.2205
173.0471.70662.533210.1665-0.17556.2390.6928-2.64632.00521.48640.3264-0.44251.99461.2995-0.91091.64330.35570.20351.48410.01761.4522-20.6655-22.010739.136
183.54443.06394.36294.95915.13786.18071.3059-3.7704-4.527-0.811-1.8928-1.26371.3862-3.2159-0.07251.22660.1330.13841.63740.16551.657-38.5891-22.811634.965
193.54540.5284-2.41633.3151-3.95145.8546-0.0726-0.7511-0.6013-1.88391.48492.21343.6957-0.5296-1.11981.2875-0.00560.08791.31740.70321.8172-38.4859-26.364422.3098
204.5451-1.26892.96625.0496-4.6066.55350.53770.1860.1186-0.1105-0.87090.22931.6358-1.24610.15911.5326-0.15160.18131.6377-0.00871.1205-37.7012-6.38141.952
217.90373.34584.81843.86574.81726.3753-1.21362.69573.6844-2.76311.53070.6739-1.0207-2.16461.1692.0398-0.3934-0.1411.30690.44561.5008-39.28360.4607-5.8403
229.3547-0.3721-0.74177.402-2.59978.1157-1.09130.1798-0.0469-0.28120.35710.2513-0.03740.27470.22821.3709-0.1668-0.12011.17090.05040.7323-32.1175-11.46082.8632
238.2082-2.90931.68592.2148-2.8013.3946-0.31051.9292-0.5189-2.98531.4517-1.59941.70441.12980.73181.98490.0760.44931.6414-0.15781.4234-29.1091-15.4462-7.0817
248.7448-1.58925.35577.12090.53029.2829-0.9748-0.0411.527-0.4873-1.7651-1.30520.07825.63830.47121.54150.07050.08391.38520.00781.1486-27.4088-7.905410.2184
257.71547.20582.47617.73944.20893.16490.31540.1060.15941.0166-0.37741.58550.5756-0.74490.65181.3990.020.08011.56030.19061.5508-41.5177-12.585521.8158
266.9989-4.6505-6.70474.58494.1175.8987-1.7249-0.26170.8319-0.16850.79591.9606-0.6340.99210.85521.3753-0.09520.00011.28210.03121.6042-36.1649-10.110514.9906
276.5075-1.8031-2.25768.8117-6.69626.59080.24460.2442-0.0791-0.28590.12621.73120.5866-0.1285-0.45921.2213-0.0521-0.06751.2898-0.12051.3639-44.5984-4.727110.0032
282.0132-1.3712-6.07485.92115.66437.44490.6391-0.97914.21892.23224.2663-1.55610.45721.7119-0.56051.50360.4791-0.21272.64960.31241.9786-9.94512.8147.5111
293.96590.7019-3.14253.86522.84415.3738-1.31372.81631.171-2.40020.37051.1509-2.14397.33210.71342.5262-0.2287-0.00463.140.27261.7205-1.28387.6442-7.8168
306.1273-2.331-2.49423.32340.07175.790.16491.9145-1.1325-1.4320.1651-0.5413-0.28841.6483-0.21321.8989-0.03770.14621.87430.11871.6905-13.87032.8022-2.11
316.80383.427-3.96313.0789-4.02485.34321.52670.05741.3663-2.6822-2.04120.9810.88650.26710.24552.0390.0191-0.09571.744-0.23081.9723-15.404113.0904-6.5628
326.10552.56011.01093.24090.65156.1028-0.4293.77432.8318-3.39511.0656-1.9181.2014-0.8095-0.45562.8244-0.75930.61162.29840.26752.0147-30.3265-1.8544-9.5171
331.8155.02853.44231.0510.84690.5665-2.29551.54984.06940.40821.2912-0.38842.33970.1513-1.65793.52330.19070.49421.42520.47140.927-37.14-17.5754-9.0365
349.2192.9927-5.12022.6104-1.59514.9420.01261.3426-2.5152-0.2869-0.32031.49392.71212.18131.1812.3297-0.07350.00381.32730.07161.8251-41.7196-21.36165.6394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 33 )
4X-RAY DIFFRACTION4chain 'A' and (resid 34 through 49 )
5X-RAY DIFFRACTION5chain 'A' and (resid 50 through 66 )
6X-RAY DIFFRACTION6chain 'A' and (resid 67 through 73 )
7X-RAY DIFFRACTION7chain 'A' and (resid 74 through 90 )
8X-RAY DIFFRACTION8chain 'A' and (resid 91 through 108 )
9X-RAY DIFFRACTION9chain 'A' and (resid 109 through 122 )
10X-RAY DIFFRACTION10chain 'A' and (resid 123 through 132 )
11X-RAY DIFFRACTION11chain 'B' and (resid 0 through 4 )
12X-RAY DIFFRACTION12chain 'B' and (resid 5 through 9 )
13X-RAY DIFFRACTION13chain 'B' and (resid 10 through 14 )
14X-RAY DIFFRACTION14chain 'B' and (resid 15 through 20 )
15X-RAY DIFFRACTION15chain 'B' and (resid 21 through 28 )
16X-RAY DIFFRACTION16chain 'B' and (resid 29 through 42 )
17X-RAY DIFFRACTION17chain 'B' and (resid 43 through 56 )
18X-RAY DIFFRACTION18chain 'B' and (resid 57 through 61 )
19X-RAY DIFFRACTION19chain 'B' and (resid 62 through 68 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1 through 17 )
21X-RAY DIFFRACTION21chain 'C' and (resid 18 through 28 )
22X-RAY DIFFRACTION22chain 'C' and (resid 29 through 49 )
23X-RAY DIFFRACTION23chain 'C' and (resid 50 through 66 )
24X-RAY DIFFRACTION24chain 'C' and (resid 67 through 73 )
25X-RAY DIFFRACTION25chain 'C' and (resid 74 through 95 )
26X-RAY DIFFRACTION26chain 'C' and (resid 96 through 108 )
27X-RAY DIFFRACTION27chain 'C' and (resid 109 through 132 )
28X-RAY DIFFRACTION28chain 'D' and (resid -2 through 4 )
29X-RAY DIFFRACTION29chain 'D' and (resid 5 through 14 )
30X-RAY DIFFRACTION30chain 'D' and (resid 15 through 34 )
31X-RAY DIFFRACTION31chain 'D' and (resid 35 through 42 )
32X-RAY DIFFRACTION32chain 'D' and (resid 43 through 52 )
33X-RAY DIFFRACTION33chain 'D' and (resid 53 through 62 )
34X-RAY DIFFRACTION34chain 'D' and (resid 63 through 68 )

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