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

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Basic information

Entry
Database: PDB / ID: 9qdj
TitleCRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD018870911
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 / MOLECULAR REPLACEMENT / Resolution: 2.597 Å
AuthorsDawson, A. / Cleghorn, L.A.T. / Davis, S.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1066891 United States
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 6, 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)58,6353
Polymers58,1901
Non-polymers4452
Water21612
1
A: Lysine--tRNA ligase 1
hetero molecules

A: Lysine--tRNA ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2706
Polymers116,3792
Non-polymers8914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)83.701, 83.701, 147.691
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-A1I60 / 2-azanyl-6-[(1~{S})-2,2-bis(fluoranyl)cyclohexyl]-4-methoxy-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one


Mass: 298.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16F2N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 44.78 % / 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 tempearature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 3, 2018
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.59→46.225 Å / Num. obs: 16852 / % possible obs: 99.7 % / Redundancy: 11.2 % / Biso Wilson estimate: 51.64 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.36 / Rpim(I) all: 0.161 / Χ2: 0.85 / Net I/σ(I): 4.8
Reflection shellResolution: 2.6→2.71 Å / Redundancy: 9.6 % / Rmerge(I) obs: 2.404 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1977 / CC1/2: 0.589 / Rpim(I) all: 0.808 / Χ2: 0.56 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.597→46.225 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.873 / SU B: 20.153 / SU ML: 0.404 / Cross valid method: FREE R-VALUE / ESU R: 1.169 / ESU R Free: 0.404
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3181 843 5.019 %
Rwork0.2601 15953 -
all0.263 --
obs-16796 99.555 %
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: 64.121 Å2
Baniso -1Baniso -2Baniso -3
1-2.824 Å2-0 Å2-0 Å2
2--2.824 Å2-0 Å2
3----5.648 Å2
Refinement stepCycle: LAST / Resolution: 2.597→46.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3627 0 31 12 3670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123724
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163600
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.8345056
X-RAY DIFFRACTIONr_angle_other_deg0.461.7618248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2545462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.6535.34144
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.043101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96610613
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.12510167
X-RAY DIFFRACTIONr_chiral_restr0.060.2581
X-RAY DIFFRACTIONr_chiral_restr_other0.0170.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024453
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02863
X-RAY DIFFRACTIONr_nbd_refined0.2180.2754
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.23313
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21780
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22024
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.296
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0660.229
X-RAY DIFFRACTIONr_nbd_other0.1660.2157
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.180.218
X-RAY DIFFRACTIONr_mcbond_it4.1896.4321869
X-RAY DIFFRACTIONr_mcbond_other4.186.4311869
X-RAY DIFFRACTIONr_mcangle_it6.69711.5352324
X-RAY DIFFRACTIONr_mcangle_other6.69611.5342325
X-RAY DIFFRACTIONr_scbond_it4.0426.581855
X-RAY DIFFRACTIONr_scbond_other4.0416.5791856
X-RAY DIFFRACTIONr_scangle_it6.49212.0212732
X-RAY DIFFRACTIONr_scangle_other6.49112.0192733
X-RAY DIFFRACTIONr_lrange_it9.88462.3514009
X-RAY DIFFRACTIONr_lrange_other9.88462.3514009
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
2.597-2.6640.41590.38111040.38312010.8680.8796.8360.371
2.664-2.7370.428600.35211370.35611980.8870.88799.91650.345
2.737-2.8160.394560.36410890.36611450.8940.8941000.344
2.816-2.9030.385720.34210510.34511240.9040.91199.9110.318
2.903-2.9970.339560.30510280.30710880.8880.92999.63240.282
2.997-3.1020.298520.27510160.27610700.9450.94599.81310.251
3.102-3.2190.362600.2799510.28410110.9120.9451000.254
3.219-3.3490.287450.2639500.2659960.9460.95499.89960.247
3.349-3.4970.272410.2759030.2759450.9610.95899.89420.257
3.497-3.6670.306410.2618560.2638970.9360.9591000.249
3.667-3.8640.292330.2558310.2568650.9290.95899.88440.237
3.864-4.0970.381340.2657930.2698310.9230.95399.51870.241
4.097-4.3770.334460.2337330.2397830.9260.96699.48910.226
4.377-4.7240.245410.2166890.2187350.9630.96999.31970.214
4.724-5.170.337320.2276380.2326710.9390.96899.8510.224
5.17-5.7710.329210.2415910.2446130.9430.96899.83690.239
5.771-6.6470.289340.2425280.2455640.9530.96899.64540.24
6.647-8.0990.339280.2024540.2084830.940.97499.7930.205
8.099-11.2810.151160.1813730.183920.9820.98199.23470.204
11.281-46.2250.362160.3062380.3082550.9140.92399.60780.325

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