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- PDB-7f7n: Solution structure of apo-WhiB4 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 7f7n
TitleSolution structure of apo-WhiB4 from Mycobacterium tuberculosis
ComponentsTranscriptional regulator WhiB4
KeywordsDNA BINDING PROTEIN / apo-WhiB4 / helix-turn-helix domain / intrinsically disordered domain
Function / homology
Function and homology information


dinitrosyl-iron complex binding / protein-disulfide reductase [NAD(P)H] activity / cell redox homeostasis / peptidoglycan-based cell wall / 4 iron, 4 sulfur cluster binding / negative regulation of DNA-templated transcription / DNA binding / metal ion binding / cytoplasm
Similarity search - Function
Transcription factor WhiB / WhiB-like iron-sulfur binding domain / Transcription factor WhiB / 4Fe-4S WhiB-like (Wbl)-type iron-sulfur binding domain profile.
Similarity search - Domain/homology
Transcriptional regulator WhiB4
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsXia, B. / Duan, B.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0501202 China
National Natural Science Foundation of China (NSFC)31570734 China
Citation
Journal: Magn Reson Lett / Year: 2022
Title: DNA binding mechanism of WhiB4 from Mycobacterium tuberculosis
Authors: Zhai, Q. / Duan, B. / Lin, C. / Liu, J. / Zhang, L. / Xia, B.
#1: Journal: Biomol.Nmr Assign. / Year: 2021
Title: 1H, 13C, and 15N resonance assignments of reduced apo-WhiB4 from Mycobacterium tuberculosis
Authors: Zhai, Q. / Lin, C. / Duan, B. / Liu, J. / Zhang, L. / Xia, B.
History
DepositionJun 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator WhiB4


Theoretical massNumber of molelcules
Total (without water)14,3051
Polymers14,3051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Monomer
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcriptional regulator WhiB4


Mass: 14305.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: whiB4, Rv3681c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WF39

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-13C HSQC
121isotropic22D 1H-15N HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D CCHCOSY
171isotropic23D 1H-15N NOESY
161isotropic23D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.4 mM [U-100% 13C; U-100% 15N] WhiB4, 95% H2O/5% D2O
Details: The NMR samples containing 0.4 mM reduced apo-WhiB4 in 50 mM Tris-HCl buffer (pH 7.0) with 95% H2O/5% D2O, along with 50 mM NaCl, 20 mM DTT, 0.03% NaN3, 0.01% DSS and 5% tablet of EDTA-free ...Details: The NMR samples containing 0.4 mM reduced apo-WhiB4 in 50 mM Tris-HCl buffer (pH 7.0) with 95% H2O/5% D2O, along with 50 mM NaCl, 20 mM DTT, 0.03% NaN3, 0.01% DSS and 5% tablet of EDTA-free protease inhibitor cocktail (Roche)
Label: 15N_13C_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.4 mM / Component: WhiB4 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsDetails: 50 mM Tris-HCl buffer, 50 mM NaCl, 20 mM DTT, 0.03% NaN3, 0.01% DSS, and 5% tablet of EDTA-free protease inhibitor cocktail (Roche)
Ionic strength: 50 mM NaCl mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD7001
Bruker AVANCE III HDBrukerAVANCE III HD9502

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Processing

NMR software
NameDeveloperClassification
SANEDuggan, Legge, Dyson & Wrightrefinement
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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