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- PDB-7r5a: Vibrio cholera ParD2:ParE2 antitoxin:toxin complex -

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Basic information

Entry
Database: PDB / ID: 7r5a
TitleVibrio cholera ParD2:ParE2 antitoxin:toxin complex
Components
  • Antitoxin ParD
  • Toxin
KeywordsTOXIN / Prokaryotic Toxin:Antitoxin System / intrinsically disordered proteins / RHH protein / DNA binding protein / transcriptional repressor / Antitoxin / Gyrase-poison / Vibrio cholerae
Function / homology
Function and homology information


detoxification / toxin sequestering activity / regulation of DNA-templated transcription
Similarity search - Function
Toxin-antitoxin system, toxin component ParE1/4 / Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH / Antitoxin ParD / Antitoxin ParD superfamily / : / ParE toxin of type II toxin-antitoxin system, parDE / Toxin-antitoxin system, RelE/ParE toxin family / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Ribbon-helix-helix
Similarity search - Domain/homology
Antitoxin ParD / Toxin
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsGarcia-Rodriguez, G. / Loris, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Sci Adv / Year: 2024
Title: Toxin:antitoxin ratio sensing autoregulation of the Vibrio cholerae parDE2 module.
Authors: Garcia-Rodriguez, G. / Girardin, Y. / Kumar Singh, R. / Volkov, A.N. / Van Dyck, J. / Muruganandam, G. / Sobott, F. / Charlier, D. / Loris, R.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Entropic pressure controls the oligomerization of the Vibrio cholerae ParD2 antitoxin.
Authors: Garcia-Rodriguez, G. / Girardin, Y. / Volkov, A.N. / Singh, R.K. / Muruganandam, G. / Van Dyck, J. / Sobott, F. / Versees, W. / Charlier, D. / Loris, R.
History
DepositionFeb 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin
B: Antitoxin ParD
C: Antitoxin ParD
D: Antitoxin ParD


Theoretical massNumber of molelcules
Total (without water)39,3544
Polymers39,3544
Non-polymers00
Water00
1
A: Toxin
B: Antitoxin ParD
C: Antitoxin ParD
D: Antitoxin ParD

A: Toxin
B: Antitoxin ParD
C: Antitoxin ParD
D: Antitoxin ParD


Theoretical massNumber of molelcules
Total (without water)78,7078
Polymers78,7078
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area18590 Å2
ΔGint-97 kcal/mol
Surface area25420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.780, 65.780, 127.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Toxin


Mass: 12435.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: VC_A0359 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KMJ0
#2: Protein Antitoxin ParD


Mass: 8972.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: parD, VC_A0360.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P58093

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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: 1.75 Å3/Da / Density % sol: 29.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Potassium chloride, 0.1 M Sodium HEPES, pH 7, 15 % PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.95→46.51 Å / Num. obs: 78228 / % possible obs: 99.81 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1628 / Net I/σ(I): 10.62
Reflection shellResolution: 2.95→3.056 Å / Num. unique obs: 7628 / CC1/2: 0.512

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kxe

3kxe


Resolution: 2.95→46.51 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 32.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3081 1105 9.83 %
Rwork0.2632 10138 -
obs0.2676 11243 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 218.72 Å2 / Biso mean: 98.0618 Å2 / Biso min: 43.5 Å2
Refinement stepCycle: final / Resolution: 2.95→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 0 0 2069
Num. residues----262
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.080.37731140.37571281139599
3.08-3.250.34551700.364412271397100
3.25-3.450.37371170.348213031420100
3.45-3.720.3721730.30112241397100
3.72-4.090.38881110.271213121423100
4.09-4.680.29931620.246612351397100
4.68-5.890.29441090.239313041413100
5.9-46.510.25041490.218612521401100
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)
15.6202-2.4823-3.3546.26251.00388.439-0.349-0.48290.08680.16130.21760.0139-0.80290.33270.12950.34440.0138-0.16020.65610.02320.429913.48497.845710.0404
27.03890.05260.25271.5818-0.42372.0399-0.2722-0.7858-0.76690.09610.0131-0.092-0.0625-0.12060.25920.53710.1706-0.06320.56150.00660.469-2.8707-1.411812.5451
35.80920.5280.92812.848-2.11152.6182-0.0375-0.54310.461-0.31560.1917-0.28361.66780.74320.17120.99420.2824-0.04730.9494-0.05750.7562-16.1627-1.054317.136
43.3609-1.77370.86977.6793-5.50688.6345-0.3493-0.4611-0.52330.4320.23790.245-0.31190.53730.18230.4471-0.00260.02220.51710.0090.8616-15.0681-14.21970.8619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A2 - 95
2X-RAY DIFFRACTION2chain 'B'B6 - 78
3X-RAY DIFFRACTION3chain 'C'C6 - 51
4X-RAY DIFFRACTION4chain 'D'D5 - 53

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