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- PDB-8b4c: ToxR bacterial transcriptional regulator bound to 20 bp toxT prom... -

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Basic information

Entry
Database: PDB / ID: 8b4c
TitleToxR bacterial transcriptional regulator bound to 20 bp toxT promoter DNA
Components
  • (DNA (20-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: 2.07 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
D: Cholera toxin transcriptional activator
L: DNA (20-MER)
M: DNA (20-MER)


Theoretical massNumber of molelcules
Total (without water)24,9653
Polymers24,9653
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-27 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.500, 54.209, 63.657
Angle α, β, γ (deg.)90.00, 92.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cholera toxin transcriptional activator


Mass: 12703.462 Da / Num. of mol.: 1
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 (20-MER)


Mass: 6096.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)
#3: DNA chain DNA (20-MER)


Mass: 6165.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 4000, 0.1 M sodium acetate pH 4, 0.15 M ammonium acetate

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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: Oct 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.07→63.59 Å / Num. obs: 14625 / % possible obs: 99.82 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 16.32
Reflection shellResolution: 2.07→2.14 Å / Rmerge(I) obs: 1.016 / Num. unique obs: 1451

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PhoB DNA binding domain (1GXP)

1gxp


Resolution: 2.07→63.59 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.094 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24107 734 4.8 %RANDOM
Rwork0.1823 ---
obs0.18494 14625 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.446 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0 Å2-0.68 Å2
2---2.29 Å2-0 Å2
3---3.15 Å2
Refinement stepCycle: 1 / Resolution: 2.07→63.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms886 814 0 177 1877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0151813
X-RAY DIFFRACTIONr_bond_other_d0.0020.021338
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.5492619
X-RAY DIFFRACTIONr_angle_other_deg1.22633118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8095107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07924.09144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83915175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.186158
X-RAY DIFFRACTIONr_chiral_restr0.0940.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021456
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02374
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5352.846431
X-RAY DIFFRACTIONr_mcbond_other2.5262.842430
X-RAY DIFFRACTIONr_mcangle_it3.5534.248537
X-RAY DIFFRACTIONr_mcangle_other3.5494.253538
X-RAY DIFFRACTIONr_scbond_it3.9384.0061382
X-RAY DIFFRACTIONr_scbond_other3.9364.0061383
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8265.9752083
X-RAY DIFFRACTIONr_long_range_B_refined7.88233.3352436
X-RAY DIFFRACTIONr_long_range_B_other7.84333.2392376
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.119 Å
RfactorNum. reflection% reflection
Rfree0.238 52 -
Rwork0.239 1075 -
obs--99.38 %

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