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- PDB-8c24: ParDE1 toxin-antitoxin complex from Mycobacterium tuberculosis (r... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8c24
TitleParDE1 toxin-antitoxin complex from Mycobacterium tuberculosis (rv1960c-rv1959c)
Components
  • Antitoxin ParD1
  • Toxin ParE1
KeywordsTOXIN / Toxin-antitoxin system Gyrase inhibitor Tuberculosis
Function / homology
Function and homology information


detoxification / symbiont-mediated perturbation of host process / 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
Toxin ParE1 / Antitoxin ParD1
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 ParE1
B: Toxin ParE1
C: Antitoxin ParD1
D: Antitoxin ParD1
E: Antitoxin ParD1
F: Antitoxin ParD1


Theoretical massNumber of molelcules
Total (without water)59,6526
Polymers59,6526
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15560 Å2
ΔGint-68 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.560, 125.450, 52.260
Angle α, β, γ (deg.)90.000, 109.230, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Toxin ParE1


Mass: 11317.714 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: parE1, Rv1959c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WHG7
#2: Protein
Antitoxin ParD1


Mass: 9254.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: parD1, Rv1960c, MTCY09F9.04 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WIJ7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350 0.2 M Sodium nitrate 0.1 M Bis-tris propane pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→45.92 Å / Num. obs: 31537 / % possible obs: 99.57 % / Redundancy: 2 % / Biso Wilson estimate: 39.49 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.13
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 3147 / CC1/2: 0.669 / % possible all: 99.05

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Processing

Software
NameVersionClassification
REFMAC1.14_3260refinement
PHENIX1.14_3260refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KXE

3kxe


Resolution: 2.1→45.92 Å / SU ML: 0.2546 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2882 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2354 1552 4.94 %
Rwork0.2064 29892 -
obs0.2079 31444 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.84 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 0 0 80 3584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773558
X-RAY DIFFRACTIONf_angle_d0.884789
X-RAY DIFFRACTIONf_chiral_restr0.327512
X-RAY DIFFRACTIONf_plane_restr0.0051639
X-RAY DIFFRACTIONf_dihedral_angle_d18.3931337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.35821370.30312680X-RAY DIFFRACTION99.02
2.17-2.250.23671330.25762718X-RAY DIFFRACTION99.13
2.25-2.340.26591430.22942700X-RAY DIFFRACTION99.3
2.34-2.440.27991450.22042691X-RAY DIFFRACTION99.4
2.44-2.570.28351270.22792713X-RAY DIFFRACTION99.58
2.57-2.730.25681460.21842722X-RAY DIFFRACTION99.72
2.73-2.940.26121290.22122731X-RAY DIFFRACTION99.58
2.94-3.240.24711390.21882735X-RAY DIFFRACTION99.93
3.24-3.710.20631650.20362705X-RAY DIFFRACTION99.93
3.71-4.670.2291420.18272735X-RAY DIFFRACTION99.93
4.67-45.920.21351460.18782762X-RAY DIFFRACTION99.86

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