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- PDB-2kue: NMR structure of the PASTA domain 2 and 3 of Mycobacterium tuberc... -

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Basic information

Entry
Database: PDB / ID: 2kue
TitleNMR structure of the PASTA domain 2 and 3 of Mycobacterium tuberculosis of PknB
ComponentsSerine/threonine-protein kinase pknB
KeywordsTRANSFERASE / kinase / external domain / signaling / STPK / resuscitation / Serine/threonine-protein kinase
Function / homology
Function and homology information


negative regulation of growth rate / negative regulation of fatty acid biosynthetic process / acetyltransferase activator activity / response to host immune response / membrane => GO:0016020 / peptidoglycan biosynthetic process / protein serine/threonine/tyrosine kinase activity / peptidoglycan-based cell wall / regulation of cell shape / manganese ion binding ...negative regulation of growth rate / negative regulation of fatty acid biosynthetic process / acetyltransferase activator activity / response to host immune response / membrane => GO:0016020 / peptidoglycan biosynthetic process / protein serine/threonine/tyrosine kinase activity / peptidoglycan-based cell wall / regulation of cell shape / manganese ion binding / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / ATP binding / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Trypsin Inhibitor V; Chain A - #20 / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Trypsin Inhibitor V; Chain A / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Trypsin Inhibitor V; Chain A - #20 / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Trypsin Inhibitor V; Chain A / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PknB / Serine/threonine-protein kinase PknB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / restrained molecular dynamics in a hydrated environment
Model detailslowest energy, model 1
AuthorsBarthe, P. / Mukamolova, G. / Roumestand, C. / Cohen-Gonsaud, M.
CitationJournal: Structure / Year: 2010
Title: The structure of PknB extracellular PASTA domain from mycobacterium tuberculosis suggests a ligand-dependent kinase activation
Authors: Barthe, P. / Mukamolova, G.V. / Roumestand, C. / Cohen-Gonsaud, M.
History
DepositionFeb 17, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 14, 2010Provider: 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
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _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 15, 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: Serine/threonine-protein kinase pknB


Theoretical massNumber of molelcules
Total (without water)14,2391
Polymers14,2391
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 #1lowest energy

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Components

#1: Protein Serine/threonine-protein kinase pknB / PknB


Mass: 14238.938 Da / Num. of mol.: 1 / Fragment: PASTA domains 2 and 3, RESIDUES 423-557
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0014c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A5S4, UniProt: P9WI81*PLUS, non-specific serine/threonine protein kinase

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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
1323D HNCA
1423D HN(COCA)CB
1523D HN(CA)CB
1623D HNCO
1723D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6mM [U-100% 15N] PknB_PASTA23; 20mM sodium acetate; 95% H2O/5% D2O95% H2O/5% D2O
20.6mM [U-100% 13C; U-100% 15N] PknB_PASTA23; 20mM sodium acetate; 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMPknB_PASTA23-1[U-100% 15N]1
20 mMsodium acetate-21
0.6 mMPknB_PASTA23-3[U-100% 13C; U-100% 15N]2
20 mMsodium acetate-42
Sample conditionspH: 4.6 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance IIIBrukerAVANCE III7001
Bruker Avance IIIBrukerAVANCE III5002

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Processing

NMR softwareName: CNS / Version: 1.2 / Classification: refinement
RefinementMethod: restrained molecular dynamics in a hydrated environment
Software ordinal: 1 / Details: like RECOORD database
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 30 / Representative conformer: 1

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