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- PDB-8b4b: ToxR bacterial transcriptional regulator bound to 19 bp ompU prom... -

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Basic information

Entry
Database: PDB / ID: 8b4b
TitleToxR bacterial transcriptional regulator bound to 19 bp ompU promoter DNA
Components
  • (DNA (19-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
: / AMMONIUM ION / DNA / DNA (> 10) / Cholera toxin transcriptional activator
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

Downloads & links

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Assembly

Deposited unit
L: DNA (19-MER)
M: DNA (19-MER)
W: Cholera toxin transcriptional activator
X: Cholera toxin transcriptional activator
Y: Cholera toxin transcriptional activator
Z: Cholera toxin transcriptional activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,71032
Polymers62,9766
Non-polymers2,73426
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11380 Å2
ΔGint-212 kcal/mol
Surface area25590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.343, 60.975, 61.329
Angle α, β, γ (deg.)87.52, 89.99, 62.96
Int Tables number1
Space group name H-MP1

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Components

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DNA chain , 2 types, 2 molecules LM

#1: DNA chain DNA (19-MER)


Mass: 5753.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)
#2: DNA chain DNA (19-MER)


Mass: 5891.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)

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Protein , 1 types, 4 molecules WXYZ

#3: Protein
Cholera toxin transcriptional activator


Mass: 12832.575 Da / Num. of mol.: 4
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

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Non-polymers , 3 types, 554 molecules

#4: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.01 M cadmium chloride, 0.1 M PIPES pH 6.5, 10% ethylene glycol

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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, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→41.66 Å / Num. obs: 68439 / % possible obs: 94.94 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.68
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.713 / Num. unique obs: 6933

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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: 1.75→41.63 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 3313 4.84 %RANDOM
Rwork0.1988 ---
obs0.2005 68439 95.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 773 26 528 4846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084441
X-RAY DIFFRACTIONf_angle_d1.1196153
X-RAY DIFFRACTIONf_dihedral_angle_d22.98835
X-RAY DIFFRACTIONf_chiral_restr0.058703
X-RAY DIFFRACTIONf_plane_restr0.009650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.38211320.42372697X-RAY DIFFRACTION95
1.77-1.80.45311430.38272722X-RAY DIFFRACTION94
1.8-1.830.3781570.35322629X-RAY DIFFRACTION94
1.83-1.860.4121480.32392706X-RAY DIFFRACTION95
1.86-1.890.33261610.30262684X-RAY DIFFRACTION95
1.89-1.930.33561700.28362749X-RAY DIFFRACTION95
1.93-1.960.27961320.27342735X-RAY DIFFRACTION95
1.96-20.37621270.27292661X-RAY DIFFRACTION95
2-2.050.2751690.26722718X-RAY DIFFRACTION96
2.05-2.090.29641220.25852725X-RAY DIFFRACTION95
2.09-2.150.30681280.26172691X-RAY DIFFRACTION95
2.15-2.20.35521170.25672775X-RAY DIFFRACTION95
2.2-2.270.29931280.24742716X-RAY DIFFRACTION95
2.27-2.340.27851380.23092745X-RAY DIFFRACTION95
2.34-2.430.24551330.21112710X-RAY DIFFRACTION95
2.43-2.520.23951190.19722738X-RAY DIFFRACTION95
2.52-2.640.25291550.20372680X-RAY DIFFRACTION95
2.64-2.780.22981190.19712719X-RAY DIFFRACTION95
2.78-2.950.24841140.18822706X-RAY DIFFRACTION94
2.95-3.180.25381550.19272697X-RAY DIFFRACTION95
3.18-3.50.25471290.18992702X-RAY DIFFRACTION95
3.5-40.18531350.15772757X-RAY DIFFRACTION96
4.01-5.040.17491400.14932718X-RAY DIFFRACTION95
5.04-41.630.16741420.16982746X-RAY DIFFRACTION96

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