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- PDB-8b4e: ToxR bacterial transcriptional regulator bound to 25 bp toxT prom... -

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Basic information

Entry
Database: PDB / ID: 8b4e
TitleToxR bacterial transcriptional regulator bound to 25 bp toxT promoter DNA
Components
  • (DNA (25-MER)) x 2
  • Cholera toxin transcriptional activator
KeywordsDNA BINDING PROTEIN / bacterial transcription / activation complex
Function / homology
Function and homology information


phosphorelay response regulator activity / regulation of DNA-templated transcription / DNA binding / plasma membrane
Similarity search - Function
OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Cholera toxin transcriptional activator
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsCanals, A. / Pieretti, S. / Muriel, M. / El Yaman, N. / Fabrega-Ferrer, M. / Perez-Luque, R. / Krukonis, E.S. / Coll, M.
Funding support Spain, 4items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2014-53550-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-83720-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-120141GB- I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesMDM-2014-0435 Spain
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: ToxR activates the Vibrio cholerae virulence genes by tethering DNA to the membrane through versatile binding to multiple sites.
Authors: Canals, A. / Pieretti, S. / Muriel-Masanes, M. / El Yaman, N. / Plecha, S.C. / Thomson, J.J. / Fabrega-Ferrer, M. / Perez-Luque, R. / Krukonis, E.S. / Coll, M.
History
DepositionSep 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cholera toxin transcriptional activator
B: Cholera toxin transcriptional activator
L: DNA (25-MER)
M: DNA (25-MER)


Theoretical massNumber of molelcules
Total (without water)40,7584
Polymers40,7584
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-28 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.669, 162.366, 86.628
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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Components

#1: Protein Cholera toxin transcriptional activator


Mass: 12703.462 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: toxR, VC_0984 / Production host: Escherichia coli (E. coli) / References: UniProt: P15795
#2: DNA chain DNA (25-MER)


Mass: 7634.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)
#3: DNA chain DNA (25-MER)


Mass: 7716.066 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)

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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: 3.62 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 4000, 0.3 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.25→81.18 Å / Num. obs: 9545 / % possible obs: 99.17 % / Redundancy: 4 % / Biso Wilson estimate: 116.07 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.02
Reflection shellResolution: 3.25→3.36 Å / Rmerge(I) obs: 0.533 / Num. unique obs: 889

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Processing

Software
NameVersionClassification
PHENIX1.20rc4_4425refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB in deposition

Resolution: 3.25→81.18 Å / SU ML: 0.5785 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.8886
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 463 4.85 %RANDOM
Rwork0.2257 9082 --
obs0.2273 9545 98.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.73 Å2
Refinement stepCycle: LAST / Resolution: 3.25→81.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 1019 0 0 2782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242935
X-RAY DIFFRACTIONf_angle_d1.42274179
X-RAY DIFFRACTIONf_chiral_restr0.0734474
X-RAY DIFFRACTIONf_plane_restr0.0169359
X-RAY DIFFRACTIONf_dihedral_angle_d30.4091725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.720.39031480.33772968X-RAY DIFFRACTION98.95
3.72-4.680.31631500.25433016X-RAY DIFFRACTION99.34
4.68-81.180.20341650.18553098X-RAY DIFFRACTION98.46

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