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- PDB-6f2x: Structural characterization of the Mycobacterium tuberculosis Pro... -

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Basic information

Entry
Database: PDB / ID: 6f2x
TitleStructural characterization of the Mycobacterium tuberculosis Protein Tyrosine Kinase A (PtkA)
ComponentsProtein Tyrosine Kinase A
KeywordsTRANSFERASE / tyrosine kinase phosphorylation Mycobacterium tuberculosis
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases / protein autophosphorylation / protein tyrosine kinase activity / ATP binding / cytosol
Similarity search - Function
: / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Phosphoglycolate phosphatase-like, domain 2 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase PtkA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing with torsion angle dynamics / cartesian angle dynamics / molecular dynamics
AuthorsNiesteruk, A. / Jonker, H.R.A. / Sreeramulu, S. / Richter, C. / Hutchison, M. / Linhard, V. / Schwalbe, H.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationMacromolecular Complexes Germany
European CommissioniNext - 653706
State of HesseBMRZ Germany
Citation
Journal: J. Biol. Chem. / Year: 2018
Title: The domain architecture of PtkA, the first tyrosine kinase fromMycobacterium tuberculosis, differs from the conventional kinase architecture.
Authors: Niesteruk, A. / Jonker, H.R.A. / Richter, C. / Linhard, V. / Sreeramulu, S. / Schwalbe, H.
#1: Journal: FEBS Lett. / Year: 2018
Title: Structural characterization of the intrinsically disordered domain of Mycobacterium tuberculosis protein tyrosine kinase A.
Authors: Niesteruk, A. / Hutchison, M. / Sreeramulu, S. / Jonker, H.R.A. / Richter, C. / Abele, R. / Bock, C. / Schwalbe, H.
History
DepositionNov 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Sep 11, 2019Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.4Jun 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 1.5Jun 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: Protein Tyrosine Kinase A


Theoretical massNumber of molelcules
Total (without water)22,8751
Polymers22,8751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12020 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein Tyrosine Kinase A


Mass: 22874.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: Rv2232, MTCY427.13/MTCY427.14 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WPI9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic42D 1H-15N HSQC
123isotropic52D 1H-15N HSQC
234isotropic32D 1H-15N HSQC
141isotropic13D HNHA
152isotropic13D HNCA
162isotropic13D HN(CO)CA
172isotropic53D HN(CA)CB
182isotropic53D HN(COCA)CB
192isotropic53D HNCO
1102isotropic13D HCC(CO)NH
1112isotropic13D CC(CO)NH
1122isotropic13D (H)CCH-TOCSY
1131isotropic43D 1H-15N NOESY
1142isotropic52D 1H-13C HSQC aliphatic
1242isotropic42D 1H-13C HSQC aromatic
1172isotropic53D 1H-13C NOESY aliphatic
1182isotropic43D 1H-13C NOESY aromatic
1191isotropic22D 1H-15N HETNOE
1201isotropic22D 1H-15N T1
1211isotropic22D 1H-15N T2
1221isotropic22D 1H-15N IPAP-HSQC
1231anisotropic22D 1H-15N IPAP-HSQC
2255isotropic33D HN(CA)CB
2265isotropic33D HN(CA)NNH
2274isotropic33D 1H-15N NOESY
2285isotropic33D HNCO
2294isotropic13D HNHA
1303isotropic53D HN(CA)CB
1313isotropic53D HN(COCA)CB
1323isotropic53D HNCO
1333isotropic53D HN(CA)CO

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.2 mM [U-15N] PtkA, 50 mM HEPES, 300 mM sodium chloride, 10 mM DTT, 10 mM magnesium chloride, 90% H2O/10% D2OC-terminal kinase core domain (KCD, 76-291) of PtkACTD (15N)90% H2O/10% D2O
solution20.2 mM [U-13C; U-15N] PtkA, 50 mM HEPES, 300 mM sodium chloride, 10 mM DTT, 10 mM magnesium chloride, 90% H2O/10% D2OC-terminal kinase core domain (KCD, 76-291) of PtkACTD (13C15N)90% H2O/10% D2O
solution30.2 mM [U-13C; U-15N; U-2H] PtkA, 50 mM HEPES, 300 mM sodium chloride, 10 mM DTT, 10 mM magnesium chloride, 90% H2O/10% D2Ofull length PtkA protein (1-291)FULL (13C15N2H)90% H2O/10% D2O
solution40.3 mM [U-15N] PtkA, 50 mM HEPES, 300 mM sodium chloride, 10 mM DTT, 10 mM magnesium chloride, 90% H2O/10% D2ON-terminal intrinsical disordered domain (IDD, 1-81) of PtkANTD (15N)90% H2O/10% D2O
solution50.3 mM [U-13C; U-15N] PtkA, 50 mM HEPES, 300 mM sodium chloride, 10 mM DTT, 10 mM magnesium chloride, 90% H2O/10% D2ON-terminal intrinsical disordered domain (IDD, 1-81) of PtkANTD (13C15N)90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMPtkA[U-15N]1
50 mMHEPESnatural abundance1
300 mMsodium chloridenatural abundance1
10 mMDTTnatural abundance1
10 mMmagnesium chloridenatural abundance1
0.2 mMPtkA[U-13C; U-15N]2
50 mMHEPESnatural abundance2
300 mMsodium chloridenatural abundance2
10 mMDTTnatural abundance2
10 mMmagnesium chloridenatural abundance2
0.2 mMPtkA[U-13C; U-15N; U-2H]3
50 mMHEPESnatural abundance3
300 mMsodium chloridenatural abundance3
10 mMDTTnatural abundance3
10 mMmagnesium chloridenatural abundance3
0.3 mMPtkA[U-15N]4
50 mMHEPESnatural abundance4
300 mMsodium chloridenatural abundance4
10 mMDTTnatural abundance4
10 mMmagnesium chloridenatural abundance4
0.3 mMPtkA[U-13C; U-15N]5
50 mMHEPESnatural abundance5
300 mMsodium chloridenatural abundance5
10 mMDTTnatural abundance5
10 mMmagnesium chloridenatural abundance5
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1354 mMnormal7.5ambient mbar298 K
2330 mMlowph2ambient mbar298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001cryoprobe
Bruker AVANCEBrukerAVANCE7002cryoprobe
Bruker AVANCEBrukerAVANCE8003cryoprobe
Bruker AVANCEBrukerAVANCE9004cryoprobe
Bruker AVANCEBrukerAVANCE9505cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
Sparky3.114Goddard and Knellerchemical shift assignment
Sparky3.114Goddard and Knellerpeak picking
Sparky3.114Goddard and Knellerdata analysis
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIA1.2 HJ development versionLinge, O'Donoghue and Nilgesrefinement
Refinement
MethodSoftware ordinalDetails
simulated annealing with torsion angle dynamics6structure determination
cartesian angle dynamics7energy minimization
molecular dynamics8refinement in water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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