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- PDB-6qkq: NMR solution structure of LSR2-T112D binding domain. -

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Basic information

Entry
Database: PDB / ID: 6qkq
TitleNMR solution structure of LSR2-T112D binding domain.
ComponentsNucleoid-associated protein Lsr2
KeywordsDNA BINDING PROTEIN / Tuberculosis / DNA oraganisation / Transcriptional regulator / PknB substrate
Function / homology
Function and homology information


cellular response to oxygen levels / DNA protection / nucleoid / response to iron ion / acyltransferase activity / peptidoglycan-based cell wall / response to hydrogen peroxide / regulation of DNA-templated transcription / DNA binding / plasma membrane / cytosol
Similarity search - Function
Lsr2 / Lsr2, dimerization domain / Lsr2 / E3-binding domain superfamily
Similarity search - Domain/homology
Nucleoid-associated protein Lsr2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / MDSA, refinement in explicit solvent
AuthorsBarthe, P. / Cohen-Gonsaud, M. / Mukamolova, G.V.
CitationJournal: Mol.Microbiol. / Year: 2019
Title: Protein kinase B controls Mycobacterium tuberculosis growth via phosphorylation of the transcriptional regulator Lsr2 at threonine 112.
Authors: Alqaseer, K. / Turapov, O. / Barthe, P. / Jagatia, H. / De Visch, A. / Roumestand, C. / Wegrzyn, M. / Bartek, I.L. / Voskuil, M.I. / O'Hare, H.M. / Ajuh, P. / Bottrill, A.R. / Witney, A.A. / ...Authors: Alqaseer, K. / Turapov, O. / Barthe, P. / Jagatia, H. / De Visch, A. / Roumestand, C. / Wegrzyn, M. / Bartek, I.L. / Voskuil, M.I. / O'Hare, H.M. / Ajuh, P. / Bottrill, A.R. / Witney, A.A. / Cohen-Gonsaud, M. / Waddell, S.J. / Mukamolova, G.V.
History
DepositionJan 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoid-associated protein Lsr2


Theoretical massNumber of molelcules
Total (without water)5,5081
Polymers5,5081
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3960 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nucleoid-associated protein Lsr2


Mass: 5508.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: lsr2, Rv3597c, MTCY07H7B.25 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WIP7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-15N NOESY
121isotropic23D 1H-15N TOCSY
132isotropic22D 1H-1H NOESY
142isotropic22D 1H-1H TOCSY
152isotropic22D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-15N] LSR2-T112D protein, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.5 mM [U-15N] LSR2-T112D protein, 100% D2OD2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMLSR2-T112D protein[U-15N]1
0.5 mMLSR2-T112D protein[U-15N]2
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 293 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
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CINDYPadillachemical shift assignment
GifaDelsucpeak picking
RefinementMethod: MDSA, refinement in explicit solvent / Software ordinal: 1 / Details: RECOORD Procedure
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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