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- PDB-7q52: Crystal structure of S/T protein kinase PknG from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 7q52
TitleCrystal structure of S/T protein kinase PknG from Mycobacterium tuberculosis in complex with inhibitor L2W
ComponentsSerine/threonine-protein kinase PknG
KeywordsTRANSFERASE / Tuberculosis / inhibitor / L2W
Function / homology
Function and homology information


symbiont-mediated perturbation of host signal transduction pathway / symbiont-mediated perturbation of host defenses / glutamine catabolic process / glutamate catabolic process / evasion of host immune response / protein autophosphorylation / non-specific serine/threonine protein kinase / symbiont-mediated suppression of host innate immune response / response to antibiotic / protein serine kinase activity ...symbiont-mediated perturbation of host signal transduction pathway / symbiont-mediated perturbation of host defenses / glutamine catabolic process / glutamate catabolic process / evasion of host immune response / protein autophosphorylation / non-specific serine/threonine protein kinase / symbiont-mediated suppression of host innate immune response / response to antibiotic / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Protein kinase G, rubredoxin domain / Protein kinase G rubredoxin domain / Protein kinase G, tetratricopeptide repeat containing domain / Protein kinase G tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. ...Protein kinase G, rubredoxin domain / Protein kinase G rubredoxin domain / Protein kinase G, tetratricopeptide repeat containing domain / Protein kinase G tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-8ZC / : / Serine/threonine-protein kinase PknG
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDefelipe, L.A. / Burastero, O. / Bento, I. / Garcia-Alai, M.M.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT2015-2276European Union
H2020 Marie Curie Actions of the European Commission664726European Union
CitationJournal: J.Med.Chem. / Year: 2022
Title: Cosolvent Sites-Based Discovery of Mycobacterium Tuberculosis Protein Kinase G Inhibitors.
Authors: Burastero, O. / Defelipe, L.A. / Gola, G. / Tateosian, N.L. / Lopez, E.D. / Martinena, C.B. / Arcon, J.P. / Traian, M.D. / Wetzler, D.E. / Bento, I. / Barril, X. / Ramirez, J. / Marti, M.A. ...Authors: Burastero, O. / Defelipe, L.A. / Gola, G. / Tateosian, N.L. / Lopez, E.D. / Martinena, C.B. / Arcon, J.P. / Traian, M.D. / Wetzler, D.E. / Bento, I. / Barril, X. / Ramirez, J. / Marti, M.A. / Garcia-Alai, M.M. / Turjanski, A.G.
History
DepositionNov 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: 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_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Serine/threonine-protein kinase PknG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7345
Polymers36,3351
Non-polymers3994
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-19 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.327, 37.016, 106.781
Angle α, β, γ (deg.)90.000, 105.500, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serine/threonine-protein kinase PknG


Mass: 36335.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pknG, Rv0410c, MTCY22G10.06c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WI73, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-8ZC / 2-azanyl-3-(4-fluorophenyl)carbonyl-indolizine-1-carboxamide


Mass: 297.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12FN3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Mother Liquor: 0.2M CaCl2, 0.2 M TRIS, pH 8.5 and 20 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 196 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 4, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.35→51.5 Å / Num. obs: 12303 / % possible obs: 98.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 62.8 Å2 / CC1/2: 0.999 / Net I/σ(I): 1.67
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 6.9 % / Num. unique obs: 1180 / CC1/2: 0.699 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSVERSION Feb 5, 2021data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y12

4y12


Resolution: 2.35→51.502 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.276 / WRfactor Rwork: 0.218 / SU B: 16.055 / SU ML: 0.345 / Average fsc free: 0.7643 / Average fsc work: 0.8027 / Cross valid method: FREE R-VALUE / ESU R: 0.611 / ESU R Free: 0.296 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2676 627 5.12 %
Rwork0.215 11619 -
all0.218 --
obs-12246 98.377 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 74.413 Å2
Baniso -1Baniso -2Baniso -3
1-3.035 Å20 Å21.561 Å2
2--1.17 Å20 Å2
3----4.395 Å2
Refinement stepCycle: LAST / Resolution: 2.35→51.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2401 0 25 29 2455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122490
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.643395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.15312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72121.811127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89315390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9751518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021932
X-RAY DIFFRACTIONr_nbd_refined0.2270.21112
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21713
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.292
X-RAY DIFFRACTIONr_metal_ion_refined0.1620.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.280.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3110.25
X-RAY DIFFRACTIONr_mcbond_it5.1617.3021251
X-RAY DIFFRACTIONr_mcangle_it7.62610.9391562
X-RAY DIFFRACTIONr_scbond_it5.8277.6051239
X-RAY DIFFRACTIONr_scangle_it8.40111.2281833
X-RAY DIFFRACTIONr_lrange_it12.976136.89410396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.4110.325420.374848X-RAY DIFFRACTION98.4513
2.411-2.4770.424460.367824X-RAY DIFFRACTION98.5277
2.477-2.5490.395460.354806X-RAY DIFFRACTION98.6111
2.549-2.6270.544360.362777X-RAY DIFFRACTION98.5455
2.627-2.7130.426550.319765X-RAY DIFFRACTION98.7952
2.713-2.8090.314350.321743X-RAY DIFFRACTION98.8564
2.809-2.9140.43450.306692X-RAY DIFFRACTION99.5946
2.914-3.0330.343400.28696X-RAY DIFFRACTION98.5274
3.033-3.1680.469250.246657X-RAY DIFFRACTION97.9885
3.168-3.3230.314330.248643X-RAY DIFFRACTION98.5423
3.323-3.5020.306350.268582X-RAY DIFFRACTION97.7813
3.502-3.7140.235280.241567X-RAY DIFFRACTION95.9677
3.714-3.970.264350.205536X-RAY DIFFRACTION98.11
3.97-4.2880.289260.178499X-RAY DIFFRACTION98.3146
4.288-4.6960.206210.144459X-RAY DIFFRACTION98.3607
4.696-5.2490.156150.133431X-RAY DIFFRACTION98.022
5.249-6.0590.161180.178362X-RAY DIFFRACTION97.6864
6.059-7.4140.233190.187330X-RAY DIFFRACTION99.1477
7.414-10.4580.195210.134250X-RAY DIFFRACTION99.2674

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