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- PDB-8b4d: ToxR bacterial transcriptional regulator bound to 40 bp toxT prom... -

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Basic information

Entry
Database: PDB / ID: 8b4d
TitleToxR bacterial transcriptional regulator bound to 40 bp toxT promoter DNA
Components
  • (DNA (40-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: 2.64 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
B: Cholera toxin transcriptional activator
C: Cholera toxin transcriptional activator
D: Cholera toxin transcriptional activator
L: DNA (40-MER)
M: DNA (40-MER)


Theoretical massNumber of molelcules
Total (without water)62,7255
Polymers62,7255
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9240 Å2
ΔGint-69 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.104, 42.622, 63.181
Angle α, β, γ (deg.)90.000, 105.740, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein Cholera toxin transcriptional activator


Mass: 12703.462 Da / Num. of mol.: 3
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 (40-MER)


Mass: 12260.966 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)
#3: DNA chain DNA (40-MER)


Mass: 12353.994 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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32% PEG MME 500, 0.175 M sodium chloride, 0.1 M glycine pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.64→60.57 Å / Num. obs: 16974 / % possible obs: 97.74 % / Redundancy: 3 % / Biso Wilson estimate: 63.18 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 8.86
Reflection shellResolution: 2.64→2.73 Å / Rmerge(I) obs: 0.844 / Num. unique obs: 1624

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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: 2.64→54.17 Å / SU ML: 0.4743 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 32.9591
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2796 856 5.04 %RANDOM
Rwork0.2155 16118 --
obs0.2188 16974 97.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.29 Å2
Refinement stepCycle: LAST / Resolution: 2.64→54.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 1634 0 0 4305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00994548
X-RAY DIFFRACTIONf_angle_d1.21836489
X-RAY DIFFRACTIONf_chiral_restr0.0629737
X-RAY DIFFRACTIONf_plane_restr0.0115547
X-RAY DIFFRACTIONf_dihedral_angle_d29.65991145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.80.37511470.34162650X-RAY DIFFRACTION97.8
2.8-3.020.43061300.32572649X-RAY DIFFRACTION96.69
3.02-3.320.37711560.31022611X-RAY DIFFRACTION95.94
3.32-3.80.31311400.22022700X-RAY DIFFRACTION98.82
3.81-4.790.24371360.17682742X-RAY DIFFRACTION99.04
4.79-54.170.20711470.16872766X-RAY DIFFRACTION97.13

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