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- PDB-7nmb: cytoplasmic domain of Vibrio cholerae ToxR -

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Basic information

Entry
Database: PDB / ID: 7nmb
Titlecytoplasmic domain of Vibrio cholerae ToxR
ComponentsCholera toxin transcriptional activator
KeywordsTRANSCRIPTION / DNA binding domain wHTH transcription factor
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
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
Cholera toxin transcriptional activator
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsGubensaek, N. / Zangger, K. / Hartlmueller, C. / Madl, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW9 DK Austria
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural and DNA-binding properties of the cytoplasmic domain of Vibrio cholerae transcription factor ToxR.
Authors: Gubensak, N. / Schrank, E. / Hartlmuller, C. / Gobl, C. / Falsone, F.S. / Becker, W. / Wagner, G.E. / Pulido, S. / Meyer, N.H. / Pavkov-Keller, T. / Madl, T. / Reidl, J. / Zangger, K.
History
DepositionFeb 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume / _citation.title
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cholera toxin transcriptional activator


Theoretical massNumber of molelcules
Total (without water)16,6421
Polymers16,6421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7310 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 100000back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1closest to the average

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Components

#1: Protein Cholera toxin transcriptional activator


Mass: 16641.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: toxR, ERS013165_01791 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A655QCS4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HNCA
141isotropic13D HNCO
151isotropic13D HN(CO)CA
161isotropic13D (H)CCH-TOCSY
191isotropic13D HN(CA)CB
181isotropic13D HN(CA)CO
171isotropic13D 1H-13C NOESY aromatic
1111isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY
1131isotropic1H(CCO)NH
1121isotropic1H(CCO)NH

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Sample preparation

DetailsType: solution
Contents: 400 uM [U-13C; U-15N] cToxR_1-134, 90% H2O/10% D2O
Label: 13C_15N_cToxR / Solvent system: 90% H2O/10% D2O
SampleConc.: 400 uM / Component: cToxR_1-134 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 100000 / Conformers submitted total number: 5

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