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- PDB-9h6a: Crystal structure of the E. coli F-plasmid VapBC toxin-antitoxin ... -

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Basic information

Entry
Database: PDB / ID: 9h6a
TitleCrystal structure of the E. coli F-plasmid VapBC toxin-antitoxin complex
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: 2.86 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)51,5044
Polymers51,5044
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)103,0098
Polymers103,0098
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area25890 Å2
ΔGint-107 kcal/mol
Surface area31750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.540, 90.540, 119.889
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: 10934.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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: 2.75 Å3/Da / Density % sol: 55.34 %
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: 0.98401 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98401 Å / Relative weight: 1
ReflectionResolution: 2.86→47.62 Å / Num. obs: 13589 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.149 / Rrim(I) all: 0.153 / Net I/σ(I): 16.71
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.86-2.934.6269810.2244.7471
2.93-3.023.6079800.3073.6981
3.02-3.12.8589180.4982.9311
3.1-3.22.2749240.5412.3331
3.2-3.31.4648610.7861.5021
3.3-3.421.1778780.8541.2071
3.42-3.550.8178070.9220.8381
3.55-3.690.5617940.9720.5751
3.69-3.860.3627840.9840.3711
3.86-4.050.2687330.990.2751
4.05-4.260.1836990.9960.1881
4.26-4.520.1256700.9980.1281
4.52-4.840.1046150.9980.1061
4.84-5.220.0965990.9990.0991
5.22-5.720.095380.9990.0931
5.72-6.40.0815000.9990.0831
6.4-7.390.0584360.9990.0591
7.39-9.050.04138710.0421
9.05-12.790.03330410.0341
12.79-47.620.02818110.0291

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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: 2.86→47.62 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2792 1357 10.01 %
Rwork0.2253 --
obs0.2308 13563 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.86→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 0 0 3138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053188
X-RAY DIFFRACTIONf_angle_d0.7084306
X-RAY DIFFRACTIONf_dihedral_angle_d21.2371200
X-RAY DIFFRACTIONf_chiral_restr0.046486
X-RAY DIFFRACTIONf_plane_restr0.008566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.960.33311290.35181164X-RAY DIFFRACTION98
2.96-3.080.51221370.39731222X-RAY DIFFRACTION100
3.08-3.220.38241320.33741192X-RAY DIFFRACTION100
3.22-3.390.34441350.27151202X-RAY DIFFRACTION100
3.39-3.60.30941360.27251210X-RAY DIFFRACTION100
3.6-3.880.30961380.24711210X-RAY DIFFRACTION100
3.88-4.270.25941340.22111225X-RAY DIFFRACTION100
4.27-4.890.2421370.18651217X-RAY DIFFRACTION100
4.89-6.150.29571330.24281252X-RAY DIFFRACTION100
6.17-47.620.24411460.1841312X-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)
17.4894-2.5130.73513.3495-2.10589.44090.13580.74410.93030.2341-0.1463-0.3426-0.633-0.063-0.06420.78510.1360.02420.8135-0.11120.814324.729825.776527.5944
27.5677-3.2249-0.0719.1831.84368.851-0.1967-1.2619-0.01380.70460.19240.7079-0.3818-0.3111-0.08210.90440.0281-0.00210.7225-0.07660.588424.386522.929429.6194
37.3373-0.3381-6.31567.07641.27775.5840.7338-0.69281.1011.3198-0.5814-0.08610.12030.3026-0.22840.94540.1515-0.27440.86240.07540.597132.363815.729535.6224
47.3096-0.2558-0.48721.12711.99557.170.37361.21.0264-1.11980.28240.7071-0.63620.4732-0.64561.2996-0.0253-0.17890.93030.05370.763926.636422.405910.0678
56.6068-0.2885-1.4050.9061-0.19145.57290.18050.24310.35150.07510.17460.5528-0.7061-0.5702-0.62411.22250.1243-0.17760.7854-0.05271.106428.639425.806713.1224
62.36642.4473-0.59023.13932.193.60290.4280.7127-0.689-1.3757-0.1445-0.6658-1.4878-0.26090.17361.24410.2048-0.14260.8554-0.021.154626.324832.864618.9959
75.37310.1883-2.61235.06980.98083.3825-0.23830.0422-0.1777-0.9470.64711.21560.8269-0.51410.25211.34980.3805-0.26251.0425-0.06231.128921.251733.307719.9638
82.69213.99422.76224.43443.91763.14351.7016-0.6582-2.7531-0.15170.5559-0.44770.14460.0835-2.1931.25820.04140.09981.28910.1621.34958.09550.291743.0246
94.63223.5412-0.78948.1228-2.26840.2338-0.7555-0.4007-0.23072.77970.25611.6638-1.43690.33130.01871.64110.26350.18261.4715-0.17651.07236.05513.599649.0233
104.91564.5086-3.78578.9768-4.51166.2241-0.0698-0.60040.36230.54520.06570.4662-0.27610.36150.18070.75580.16920.08930.9356-0.00230.84317.642916.160239.5313
112.4096-2.4007-2.27377.42081.34992.2151-0.7312-0.83271.2855-0.04210.51010.6348-2.24461.52890.86821.16060.0833-0.3071.28930.1631.2135.86322.625737.5476
126.74290.73113.62397.6281-0.62797.1742-1.3865-1.0419-1.2044-1.14721.3923-0.20140.031.15830.97290.89620.1772-0.05581.25540.04591.809839.47526.126422.3055
137.6011-0.1753-3.00999.4194-4.60725.03790.49950.71350.16941.3644-0.7528-1.4999-0.76620.26260.13070.9132-0.1358-0.02361.0128-0.04820.655738.38216.92022.5681
147.38472.2842-3.68623.6841-4.78996.3398-0.30280.4433-0.9007-1.05350.07580.18511.0715-0.74040.67931.2775-0.12740.17830.9371-0.14250.831238.1878-1.1297-3.4687
156.4898-0.291-0.10664.15422.40418.4794-0.05140.51180.6607-1.02980.29970.8053-1.0024-0.4775-0.03791.02540.0881-0.09490.6631-0.01270.664430.783514.44491.0664
165.28864.47130.67323.3383-0.06833.1523-0.0622-0.2725-0.68081.0144-0.2956-1.8779-0.88540.94690.14580.9667-0.1092-0.1731.0752-0.04881.194142.291112.653722.7172
175.2013-3.46261.56469.06772.99668.51650.0256-0.3070.26470.4712-0.0408-0.6310.42780.12560.16220.821-0.08420.06990.76120.0370.900442.44166.84512.3394
182.19320.7507-0.62524.73543.41543.03520.62040.0155-1.5274-1.17730.90352.9685-0.2535-1.2217-0.48661.3125-0.181-0.03791.6236-0.00421.41374.1806-10.12570.172
190.6948-1.0562-1.59141.38452.04683.0326-0.23491.99041.5721-4.27332.66411.8804-0.5255-0.8790.96591.71270.0766-0.64131.61140.32591.22572.1842-6.1064-9.5553
202.6907-2.18461.2562.8176-0.53269.0460.85241.25111.1042-0.52350.84091.9651-0.0632-1.5846-0.33241.30790.19470.06561.3933-0.01770.924113.318-0.65871.5718
211.9275-8.1224-9.73727.74977.30238.66621.8255-1.73880.3999-2.67082.09050.6055-0.54011.12310.40211.4017-0.086-0.36211.57350.07750.913717.7902-8.87-9.9668
221.895-0.892.02949.51972.18636.5063-0.31710.10550.2786-0.21010.94120.08320.23391.0263-0.6520.9375-0.17180.00641.517-0.05590.966116.234-12.2115-6.7336
233.0424-1.14752.14454.0137-6.38427.90850.67771.1066-0.3944-1.3397-0.01670.33040.30480.1979-0.73291.5138-0.0290.10390.9931-0.27780.895134.12829.689-8.6449
240.13440.5052-0.57282.09190.46333.90140.6144-0.9172-0.42810.4148-1.17552.7758-2.5880.790.09561.4246-0.4503-0.20340.9108-0.1171.472542.475921.47596.7715
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 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 90 )
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 108 )
6X-RAY DIFFRACTION6chain 'A' and (resid 109 through 122 )
7X-RAY DIFFRACTION7chain 'A' and (resid 123 through 132 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1G through 14 )
9X-RAY DIFFRACTION9chain 'B' and (resid 15 through 28 )
10X-RAY DIFFRACTION10chain 'B' and (resid 29 through 52 )
11X-RAY DIFFRACTION11chain 'B' and (resid 53 through 62 )
12X-RAY DIFFRACTION12chain 'B' and (resid 63 through 68 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 17 )
14X-RAY DIFFRACTION14chain 'C' and (resid 18 through 32 )
15X-RAY DIFFRACTION15chain 'C' and (resid 33 through 73 )
16X-RAY DIFFRACTION16chain 'C' and (resid 74 through 95 )
17X-RAY DIFFRACTION17chain 'C' and (resid 96 through 132 )
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 8 )
19X-RAY DIFFRACTION19chain 'D' and (resid 9 through 14 )
20X-RAY DIFFRACTION20chain 'D' and (resid 15 through 28 )
21X-RAY DIFFRACTION21chain 'D' and (resid 29 through 34 )
22X-RAY DIFFRACTION22chain 'D' and (resid 35 through 42 )
23X-RAY DIFFRACTION23chain 'D' and (resid 43 through 62 )
24X-RAY DIFFRACTION24chain 'D' and (resid 63 through 68 )

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