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- PDB-2kfs: NMR structure of Rv2175c -

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Basic information

Entry
Database: PDB / ID: 2kfs
TitleNMR structure of Rv2175c
ComponentsConserved hypothetical regulatory protein
KeywordsDNA BINDING PROTEIN / wHTH / DNA binding / Phosphorylation / DNA-binding protein
Function / homologyRv2175c, C-terminal / Rv2175c C-terminal domain of unknown function / peptidyl-threonine phosphorylation / DNA binding / DNA-binding protein Rv2175c
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 15
AuthorsBarthe, P. / Cohen-Gonsaud, M. / Roumestand, C. / Molle, V.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The Mycobacterium tuberculosis Ser/Thr Kinase Substrate Rv2175c Is a DNA-binding Protein Regulated by Phosphorylation.
Authors: Cohen-Gonsaud, M. / Barthe, P. / Canova, M.J. / Stagier-Simon, C. / Kremer, L. / Roumestand, C. / Molle, V.
History
DepositionFeb 27, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_keywords.text / _struct_ref_seq_dif.details
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
Revision 1.4May 8, 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: Conserved hypothetical regulatory protein


Theoretical massNumber of molelcules
Total (without water)15,9581
Polymers15,9581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 30structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Conserved hypothetical regulatory protein


Mass: 15958.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37rv / Gene: Rv2175c / Production host: Escherichia coli (E. coli) / References: UniProt: O53509

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-15N TOCSY
1332D 1H-1H NOESY
1423D HNCA
1523D CBCA(CO)NH
1623D HNCO
1723D HCACO

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Sample preparation

Details
Solution-IDContentsSolvent system
1300 mM [U-15N] Rv2175c, 10 mM sodium acetate, 150 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
2300 mM [U-13C; U-15N] Rv2175c, 10 mM sodium acetate, 150 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
3300 mM Rv2175c, 10 mM sodium acetate, 150 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 mMRv2175c[U-15N]1
10 mMsodium acetate1
150 mMsodium chloride1
300 mMRv2175c[U-13C; U-15N]2
10 mMsodium acetate2
150 mMsodium chloride2
300 mMRv2175c3
10 mMsodium acetate3
150 mMsodium chloride3
Sample conditionsIonic strength: 0.15 / pH: 4.6 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Gifa4.44Delsucprocessing
CINDY1.7aPadilladata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Procheck3.5.4Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thodata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1676 / NOE intraresidue total count: 477 / NOE long range total count: 345 / NOE medium range total count: 278 / NOE sequential total count: 576 / Hydrogen bond constraints total count: 66 / Protein chi angle constraints total count: 17 / Protein phi angle constraints total count: 95 / Protein psi angle constraints total count: 95
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 30

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