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- PDB-8c26: ParDE2 toxin-antitoxin complex from Mycobacterium tuberculosis (r... -

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Basic information

Entry
Database: PDB / ID: 8c26
TitleParDE2 toxin-antitoxin complex from Mycobacterium tuberculosis (rv2142A-rv2142c)
Components
  • Antitoxin ParD2
  • Toxin ParE2
KeywordsTOXIN / Toxin-antitoxin Gyrase inhibitor Tuberculosis
Function / homology
Function and homology information


symbiont-mediated perturbation of host process / detoxification / toxin sequestering activity
Similarity search - Function
Conserved hypothetical protein CHP02574, addiction module / : / ParE toxin of type II toxin-antitoxin system, parDE / Toxin-antitoxin system, RelE/ParE toxin family / Toxin-antitoxin system, RelE/ParE toxin domain superfamily
Similarity search - Domain/homology
Toxin ParE2 / Antitoxin ParD2
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBeck, I.N. / Blower, T.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Toxin release by conditional remodelling of ParDE1 from Mycobacterium tuberculosis leads to gyrase inhibition.
Authors: Beck, I.N. / Arrowsmith, T.J. / Grobbelaar, M.J. / Bromley, E.H.C. / Marles-Wright, J. / Blower, T.R.
History
DepositionDec 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin ParE2
B: Antitoxin ParD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3244
Polymers20,2532
Non-polymers712
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-17 kcal/mol
Surface area6900 Å2
Unit cell
Length a, b, c (Å)68.074, 68.074, 197.049
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-201-

CL

21A-202-

CL

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Components

#1: Protein Toxin ParE2


Mass: 12329.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: parE2, Rv2142c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WHG5
#2: Protein Antitoxin ParD2


Mass: 7922.755 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: parD2, Rv2142A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WJ75
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 15 % PEG 3350 0.1 M MES pH 6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.345→50.59 Å / Num. obs: 7244 / % possible obs: 94.06 % / Redundancy: 19.8 % / Biso Wilson estimate: 99.74 Å2 / CC1/2: 1 / Net I/σ(I): 7.5
Reflection shellResolution: 2.345→2.429 Å / Num. unique obs: 349 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
REFMAC1.14_3260refinement
PHENIX1.14_3260refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→50.59 Å / SU ML: 0.5185 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 41.9532 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2884 725 10.01 %
Rwork0.2539 6517 -
obs0.2575 7242 94.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.12 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 0 2 0 1023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831046
X-RAY DIFFRACTIONf_angle_d0.99491420
X-RAY DIFFRACTIONf_chiral_restr0.0608150
X-RAY DIFFRACTIONf_plane_restr0.0053189
X-RAY DIFFRACTIONf_dihedral_angle_d15.219382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.530.42051070.4409959X-RAY DIFFRACTION71.21
2.53-2.780.36461490.3761343X-RAY DIFFRACTION98.61
2.78-3.180.40831530.32961374X-RAY DIFFRACTION99.93
3.18-4.010.28651540.28481387X-RAY DIFFRACTION99.94
4.01-50.590.26621620.22041454X-RAY DIFFRACTION99.94

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