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- PDB-9qbr: CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 9qbr
TitleCRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01991231
ComponentsLysine--tRNA ligase 1
KeywordsLIGASE / inhibitor
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / LYSINE / Lysine--tRNA ligase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDawson, A. / Cleghorn, L.A.T. / Davis, S.H.
Funding support United States, United Kingdom, 3items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1066891 United States
Bill & Melinda Gates FoundationOPP1191579 United States
Wellcome Trust100195/Z/12/Z United Kingdom
CitationJournal: J.Med.Chem. / Year: 2025
Title: Design and Development of Lysyl tRNA Synthetase Inhibitors, for the Treatment of Tuberculosis.
Authors: Davis, S.H. / Mathieson, M. / Buchanan, K.I. / Dawson, A. / Smith, A. / Cocco, M. / Tamaki, F.K. / Post, J.M. / Baragana, B. / Jansen, C. / Kiczun, M. / Zuccotto, F. / Wood, G. / Scullion, P. ...Authors: Davis, S.H. / Mathieson, M. / Buchanan, K.I. / Dawson, A. / Smith, A. / Cocco, M. / Tamaki, F.K. / Post, J.M. / Baragana, B. / Jansen, C. / Kiczun, M. / Zuccotto, F. / Wood, G. / Scullion, P. / Ray, P.C. / Epemolu, O. / Lopez-Roman, E.M. / Lopez, L.G. / Engelhart, C.A. / Kim, J. / Pino, P.A. / Schnappinger, D. / Read, K.D. / Encinas, L. / Bates, R.H. / Wyatt, P.G. / Green, S.R. / Cleghorn, L.A.T.
History
DepositionMar 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine--tRNA ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6153
Polymers58,1901
Non-polymers4262
Water1,17165
1
A: Lysine--tRNA ligase 1
hetero molecules

A: Lysine--tRNA ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2306
Polymers116,3792
Non-polymers8514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area8180 Å2
ΔGint-31 kcal/mol
Surface area36830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.589, 83.589, 147.406
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Lysine--tRNA ligase 1 / Lysyl-tRNA synthetase 1 / LysRS 1


Mass: 58189.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: lysS1, lysS, Rv3598c, MTCY07H7B.24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFU9, lysine-tRNA ligase
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-A1I5H / 2-azanyl-4-methoxy-6-(4-oxidanylcyclohexyl)-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one


Mass: 278.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C13H18N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.53 % / Description: block
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Reservoir: 0.25 M NaOAc, 14% W/V PEG 3350 Protein buffer: 25 mM HEPES, 500 mM NaCl, 5% GLYCEROL, 2 mM DTT, PH 7.0,
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.4→147.41 Å / Num. obs: 21202 / % possible obs: 100 % / Redundancy: 14.4 % / Biso Wilson estimate: 57.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.254 / Rpim(I) all: 0.097 / Rrim(I) all: 0.272 / Χ2: 1.02 / Net I/σ(I): 6.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 14.1 % / Rmerge(I) obs: 5.109 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2151 / CC1/2: 0.597 / Rpim(I) all: 2.014 / Χ2: 1.05 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→72.712 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.291 / WRfactor Rwork: 0.219 / SU B: 19.235 / SU ML: 0.394 / Average fsc free: 0.8886 / Average fsc work: 0.9133 / Cross valid method: FREE R-VALUE / ESU R: 0.466 / ESU R Free: 0.321
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3081 1067 5.05 %
Rwork0.2331 20063 -
all0.237 --
obs-21130 99.915 %
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: 77.859 Å2
Baniso -1Baniso -2Baniso -3
1-4.51 Å20 Å20 Å2
2--4.51 Å20 Å2
3----9.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→72.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 30 65 3651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123649
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163539
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.8364949
X-RAY DIFFRACTIONr_angle_other_deg0.4871.7648107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3425451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.025.34144
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.385101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.38110610
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.42610164
X-RAY DIFFRACTIONr_chiral_restr0.0630.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024361
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02851
X-RAY DIFFRACTIONr_nbd_refined0.210.2820
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.23481
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21723
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2122
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.070.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.243
X-RAY DIFFRACTIONr_nbd_other0.1680.2178
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1820.222
X-RAY DIFFRACTIONr_mcbond_it5.0567.9151825
X-RAY DIFFRACTIONr_mcbond_other5.0457.9151825
X-RAY DIFFRACTIONr_mcangle_it7.89414.1992269
X-RAY DIFFRACTIONr_mcangle_other7.89214.1972270
X-RAY DIFFRACTIONr_scbond_it4.5958.1451824
X-RAY DIFFRACTIONr_scbond_other4.5948.1441825
X-RAY DIFFRACTIONr_scangle_it7.3314.8782680
X-RAY DIFFRACTIONr_scangle_other7.32814.8772681
X-RAY DIFFRACTIONr_lrange_it10.72879.0544053
X-RAY DIFFRACTIONr_lrange_other10.7379.0584046
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.4-2.4620.476650.43414640.43615320.8340.83499.80420.407
2.462-2.530.491780.41914040.42314820.7780.7831000.389
2.53-2.6030.449820.39713570.414390.7580.8191000.366
2.603-2.6830.423740.38713340.38914100.8430.85199.85820.356
2.683-2.7710.478730.37412890.37913660.8360.8699.70720.355
2.771-2.8680.391700.32412680.32813380.8510.8851000.296
2.868-2.9760.354600.27212290.27612890.9150.9241000.243
2.976-3.0970.309700.24511670.24912370.9240.9471000.221
3.097-3.2350.261520.22411190.22611710.9560.9561000.202
3.235-3.3920.239650.19410860.19711510.9460.971000.175
3.392-3.5750.273550.19110270.19510820.9420.9761000.176
3.575-3.7920.311510.18410010.19110520.940.9751000.171
3.792-4.0530.317470.1819180.1879650.9360.9761000.173
4.053-4.3760.239450.1878780.1899230.9650.9761000.182
4.376-4.7920.276380.1898060.1948440.9530.9761000.195
4.792-5.3550.263390.2357380.2367770.9520.9691000.238
5.355-6.1780.311330.226600.2256930.9350.9731000.224
6.178-7.5520.282330.1885660.1935990.950.9771000.195
7.552-10.6240.176180.164690.164870.9770.9881000.178
10.624-72.7120.37190.2832830.2883020.8910.9511000.304

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