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

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Basic information

Entry
Database: PDB / ID: 9qea
TitleCRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01839469
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: 2.3 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 7, 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)58,6133
Polymers58,1901
Non-polymers4242
Water19811
1
A: Lysine--tRNA ligase 1
hetero molecules

A: Lysine--tRNA ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2266
Polymers116,3792
Non-polymers8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)84.999, 84.999, 148.045
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-A1I61 / 2-azanyl-6-cyclohexyl-4-ethoxy-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one


Mass: 276.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.3 Å3/Da / Density % sol: 46.58 % / 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 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.3→85 Å / Num. obs: 22947 / % possible obs: 92.1 % / Redundancy: 10 % / Biso Wilson estimate: 42.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.056 / Χ2: 0.92 / Net I/σ(I): 10.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.218 / Mean I/σ(I) obs: 2 / Num. unique obs: 2376 / CC1/2: 0.96 / Rpim(I) all: 0.546 / Χ2: 0.75 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→60.176 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / SU B: 18.74 / SU ML: 0.396 / Cross valid method: FREE R-VALUE / ESU R: 0.442 / ESU R Free: 0.307
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3106 1144 5 %
Rwork0.2548 21736 -
all0.258 --
obs-22880 92.124 %
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: 72.847 Å2
Baniso -1Baniso -2Baniso -3
1-4.03 Å20 Å20 Å2
2--4.03 Å20 Å2
3----8.059 Å2
Refinement stepCycle: LAST / Resolution: 2.3→60.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3627 0 30 11 3668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123724
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163610
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.8385054
X-RAY DIFFRACTIONr_angle_other_deg0.5621.7638275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1365462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.547542
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.4851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12910623
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.71310167
X-RAY DIFFRACTIONr_chiral_restr0.0740.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024453
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02863
X-RAY DIFFRACTIONr_nbd_refined0.2360.2878
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.23720
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21793
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22097
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1140.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1690.235
X-RAY DIFFRACTIONr_nbd_other0.1520.2138
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.380.211
X-RAY DIFFRACTIONr_mcbond_it6.6947.221863
X-RAY DIFFRACTIONr_mcbond_other6.6877.221863
X-RAY DIFFRACTIONr_mcangle_it10.01412.9462320
X-RAY DIFFRACTIONr_mcangle_other10.01212.9442321
X-RAY DIFFRACTIONr_scbond_it6.2727.511861
X-RAY DIFFRACTIONr_scbond_other6.2717.5081862
X-RAY DIFFRACTIONr_scangle_it9.65213.6522734
X-RAY DIFFRACTIONr_scangle_other9.6513.652735
X-RAY DIFFRACTIONr_lrange_it13.5371.2094177
X-RAY DIFFRACTIONr_lrange_other13.52971.2044178
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
2.3-2.360.377780.40817100.40617900.8710.83399.88830.387
2.36-2.4240.44850.40516570.40717440.830.84499.88530.378
2.424-2.4940.361910.38916010.38816960.8710.85599.76420.359
2.494-2.5710.4031010.37915650.38116660.8510.8631000.352
2.571-2.6550.429560.349720.34516140.8630.89863.69270.318
2.655-2.7480.372390.3664810.36615620.7850.87133.29070.332
2.748-2.8520.413650.33614430.3415090.8820.91199.93370.313
2.852-2.9680.433770.31913670.32514450.8460.91899.93080.288
2.968-3.10.37810.27413180.27913990.8940.9421000.252
3.1-3.250.366480.25712930.26113430.8990.95199.85110.239
3.25-3.4260.367630.25612160.26112810.9090.95399.84390.244
3.426-3.6330.39570.29411560.29912180.8960.94299.58950.284
3.633-3.8830.349450.2719430.27511610.9080.94685.09910.263
3.883-4.1920.299380.268800.26210520.9410.9587.26240.259
4.192-4.590.278570.2119480.21510050.9510.9681000.219
4.59-5.1280.291440.218680.2149130.9520.97299.89050.217
5.128-5.9140.292420.2127690.2168110.9610.9751000.217
5.914-7.2260.213350.1786640.186990.9790.9781000.185
7.226-10.1460.144240.1475460.1475700.9890.9861000.161
10.146-60.1760.178180.2063390.2053570.9840.9721000.222

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