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

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Basic information

Entry
Database: PDB / ID: 9qei
TitleCRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01866774
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 / cytosol / cytoplasm
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 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,6293
Polymers58,1901
Non-polymers4402
Water46826
1
A: Lysine--tRNA ligase 1
hetero molecules

A: Lysine--tRNA ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2586
Polymers116,3792
Non-polymers8794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation8_555-y,-x,-z+1/21
MethodPISA
Unit cell
Length a, b, c (Å)83.929, 83.929, 147.289
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-A1I62 / 2-azanyl-4-ethoxy-6-[(1~{R},2~{S})-2-oxidanylcyclohexyl]-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one


Mass: 292.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.23 Å3/Da / Density % sol: 44.93 % / 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, 0.5 M NaCl, 5% glycerol, 2 mM DTT, pH 7
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.4→147.29 Å / Num. obs: 20488 / % possible obs: 96.4 % / Redundancy: 7.6 % / Biso Wilson estimate: 63.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.056 / Χ2: 1.03 / Net I/σ(I): 8.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.7 % / Rmerge(I) obs: 2.311 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2176 / CC1/2: 0.508 / Rpim(I) all: 1.17 / Χ2: 0.99 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→55.417 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.92 / SU B: 30.161 / SU ML: 0.56 / Cross valid method: FREE R-VALUE / ESU R: 0.531 / ESU R Free: 0.342
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.32 970 4.751 %
Rwork0.25 19448 -
all0.253 --
obs-20418 95.81 %
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: 89.058 Å2
Baniso -1Baniso -2Baniso -3
1-5.248 Å20 Å20 Å2
2--5.248 Å20 Å2
3----10.497 Å2
Refinement stepCycle: LAST / Resolution: 2.4→55.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 31 26 3629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123668
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163543
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.8334981
X-RAY DIFFRACTIONr_angle_other_deg0.4851.768117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3545456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.1355.34943
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.813101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.96110598
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.46310164
X-RAY DIFFRACTIONr_chiral_restr0.0620.2575
X-RAY DIFFRACTIONr_chiral_restr_other0.0040.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024390
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02850
X-RAY DIFFRACTIONr_nbd_refined0.2320.2891
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.23571
X-RAY DIFFRACTIONr_nbtor_refined0.180.21753
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22072
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1320.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1280.247
X-RAY DIFFRACTIONr_nbd_other0.1610.2175
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2010.214
X-RAY DIFFRACTIONr_mcbond_it5.3588.9311845
X-RAY DIFFRACTIONr_mcbond_other5.3558.9311845
X-RAY DIFFRACTIONr_mcangle_it8.50216.0162294
X-RAY DIFFRACTIONr_mcangle_other8.516.0142295
X-RAY DIFFRACTIONr_scbond_it4.6859.2671823
X-RAY DIFFRACTIONr_scbond_other4.6839.2651824
X-RAY DIFFRACTIONr_scangle_it7.84916.8862687
X-RAY DIFFRACTIONr_scangle_other7.84716.8842688
X-RAY DIFFRACTIONr_lrange_it11.96890.7494130
X-RAY DIFFRACTIONr_lrange_other11.96790.7484130
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
2.4-2.4620.559690.52314700.52415540.830.7799.03480.506
2.462-2.530.532730.50413970.50514930.7830.7698.45950.472
2.53-2.6030.522680.47313740.47514540.6930.75199.17470.435
2.603-2.6830.39680.46913320.46514200.830.73698.59150.421
2.683-2.770.484660.43412860.43613670.7170.80298.90270.394
2.77-2.8670.387630.38112710.38113510.8460.84798.74170.341
2.867-2.9750.404570.35212160.35512990.8370.86297.99850.303
2.975-3.0960.371640.30511630.30912410.9040.89898.87190.259
3.096-3.2340.333460.26311240.26711960.9030.9397.82610.216
3.234-3.3910.326590.2410680.24511540.9180.94997.66030.201
3.391-3.5740.358410.24110150.24610870.910.9597.14810.208
3.574-3.7890.285450.2119770.21410510.9380.96597.24070.179
3.789-4.050.239320.2175260.2189790.9710.96756.99690.189
4.05-4.3720.399470.1948560.2039280.9040.97497.3060.177
4.372-4.7870.224520.1727690.1758480.960.9896.8160.159
4.787-5.3470.289360.1937150.1987830.9380.97695.91320.176
5.347-6.1640.307320.2066320.2126960.9480.97495.40230.186
6.164-7.5260.239250.1755490.1786130.9670.9893.63780.166
7.526-10.5470.214200.1424370.1454890.9660.98893.4560.145
10.547-55.4170.28270.2492710.253060.9670.95990.84970.262

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