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- PDB-7b22: Vibrio cholerae ParD2 Antitoxin -

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Basic information

Entry
Database: PDB / ID: 7b22
TitleVibrio cholerae ParD2 Antitoxin
ComponentsAntitoxin ParD
KeywordsDNA BINDING PROTEIN / Prokaryotic Toxin-Antitoxin System / intrinsically disordered proteins / RHH protein / transcriptional repressor / Antitoxin
Function / homologyAntitoxin ParD superfamily / Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH / Antitoxin ParD / Ribbon-helix-helix / regulation of DNA-templated transcription / Antitoxin ParD
Function and homology information
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.08 Å
AuthorsGarcia-Rodriguez, G. / Loris, R.
CitationJournal: 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
DepositionNov 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antitoxin ParD
B: Antitoxin ParD
C: Antitoxin ParD
D: Antitoxin ParD
E: Antitoxin ParD
F: Antitoxin ParD
G: Antitoxin ParD
H: Antitoxin ParD


Theoretical massNumber of molelcules
Total (without water)71,7828
Polymers71,7828
Non-polymers00
Water00
1
A: Antitoxin ParD
B: Antitoxin ParD
C: Antitoxin ParD
D: Antitoxin ParD
E: Antitoxin ParD
F: Antitoxin ParD
G: Antitoxin ParD
H: Antitoxin ParD

A: Antitoxin ParD
B: Antitoxin ParD
C: Antitoxin ParD
D: Antitoxin ParD
E: Antitoxin ParD
F: Antitoxin ParD
G: Antitoxin ParD
H: Antitoxin ParD


Theoretical massNumber of molelcules
Total (without water)143,56516
Polymers143,56516
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area36530 Å2
ΔGint-189 kcal/mol
Surface area32000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.010, 101.700, 107.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Antitoxin ParD


Mass: 8972.801 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / 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: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M Lithium sulfate, 0.1 M MES pH 6 and 20 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.08→45.95 Å / Num. obs: 8845 / % possible obs: 99.5 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1738 / Net I/σ(I): 7.36
Reflection shellResolution: 3.08→3.19 Å / Rmerge(I) obs: 1.41 / Num. unique obs: 842 / CC1/2: 0.383

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kxe

3kxe


Resolution: 3.08→45.95 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2996 442 5 %
Rwork0.2706 8398 -
obs0.2721 8840 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.24 Å2 / Biso mean: 84.5736 Å2 / Biso min: 52.83 Å2
Refinement stepCycle: final / Resolution: 3.08→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 0 0 2856
Num. residues----392
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.08-3.530.34291440.31692735287999
3.53-4.440.28811470.288927812928100
4.45-45.950.29351510.248128823033100

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