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- PDB-5u94: Crystal structure of the Mycobacterium tuberculosis PASTA kinase ... -

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Basic information

Entry
Database: PDB / ID: 5u94
TitleCrystal structure of the Mycobacterium tuberculosis PASTA kinase PknB in complex with the potential theraputic kinase inhibitor GSK690693.
ComponentsSerine/threonine-protein kinase PknB
KeywordsTransferase/Transferase Inhibitor / Kinase / inhibitor / transferase / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


negative regulation of growth rate / negative regulation of fatty acid biosynthetic process / acetyltransferase activator activity / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / regulation of cell shape / manganese ion binding / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity ...negative regulation of growth rate / negative regulation of fatty acid biosynthetic process / acetyltransferase activator activity / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / regulation of cell shape / manganese ion binding / 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 / identical protein binding / plasma membrane
Similarity search - Function
PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-G93 / Serine/threonine-protein kinase PknB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWlodarchak, N. / Satyshur, K. / Striker, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UL1TR000427 United States
Hartwell Foundation United States
CitationJournal: Mol. Pharm. / Year: 2018
Title: In Silico Screen and Structural Analysis Identifies Bacterial Kinase Inhibitors which Act with beta-Lactams To Inhibit Mycobacterial Growth.
Authors: Wlodarchak, N. / Teachout, N. / Beczkiewicz, J. / Procknow, R. / Schaenzer, A.J. / Satyshur, K. / Pavelka, M. / Zuercher, W. / Drewry, D. / Sauer, J.D. / Striker, R.
History
DepositionDec 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PknB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,01411
Polymers30,8281
Non-polymers1,18710
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.786, 121.294, 49.529
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

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Components

#1: Protein Serine/threonine-protein kinase PknB


Mass: 30827.719 Da / Num. of mol.: 1 / Fragment: UNP residues 1-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pknB, Rv0014c, MTCY10H4.14c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P9WI81, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-G93 / 4-{2-(4-amino-1,2,5-oxadiazol-3-yl)-1-ethyl-7-[(3S)-piperidin-3-ylmethoxy]-1H-imidazo[4,5-c]pyridin-4-yl}-2-methylbut-3 -yn-2-ol / GSK690693


Mass: 425.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.01 %
Description: Irregular rectangle or arrowhead shape, 0.05-0.1mm average size.
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12.5% PEG 3350, 0.25M bis-tris propane pH 7.5, 0.5% glycerol, 0.1% thymidne, and 0.1% b-cyclodextran all added 1:1 with protein (9.8mg/mL) and 120uM inhibitor in 150mM NaCl, 10mM Tris pH 8. ...Details: 12.5% PEG 3350, 0.25M bis-tris propane pH 7.5, 0.5% glycerol, 0.1% thymidne, and 0.1% b-cyclodextran all added 1:1 with protein (9.8mg/mL) and 120uM inhibitor in 150mM NaCl, 10mM Tris pH 8.0, 1mM DTT, ans 1mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12717 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 23, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12717 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 20754 / % possible obs: 96.5 % / Redundancy: 12.7 % / Rsym value: 0.105 / Net I/σ(I): 23.59
Reflection shellResolution: 2.05→2.09 Å / Num. unique all: 748 / Rpim(I) all: 0.048 / % possible all: 77.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000706cdata reduction
PHENIX1.10_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O6Y

1o6y


Resolution: 2.2→41.686 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.04
RfactorNum. reflection% reflection
Rfree0.2371 1685 9.56 %
Rwork0.2008 --
obs0.2043 17624 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 238.26 Å2 / Biso mean: 83.8267 Å2 / Biso min: 45.71 Å2
Refinement stepCycle: final / Resolution: 2.2→41.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 172 44 2227
Biso mean--96.12 71.34 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022126
X-RAY DIFFRACTIONf_angle_d0.5652884
X-RAY DIFFRACTIONf_chiral_restr0.044320
X-RAY DIFFRACTIONf_plane_restr0.003375
X-RAY DIFFRACTIONf_dihedral_angle_d18.8761282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.26470.39771250.36371164128988
2.2647-2.33780.36091280.32771250137895
2.3378-2.42140.33281320.29821313144598
2.4214-2.51830.34531480.26881311145999
2.5183-2.63290.28361340.24121331146599
2.6329-2.77170.29991360.23661346148299
2.7717-2.94530.26621500.225313471497100
2.9453-3.17270.27211350.221513281463100
3.1727-3.49180.2531520.211413601512100
3.4918-3.99670.23881430.185913581501100
3.9967-5.03410.16221490.166613821531100
5.0341-41.69340.2361530.18121449160299

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