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- PDB-7qhn: CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 7qhn
TitleCRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE and an inhibitor
ComponentsLysine--tRNA ligase 1
KeywordsLIGASE / Mycobacterium tuberculosis / ATP binding
Function / homology
Function and homology information


ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA binding / magnesium ion binding / extracellular space ...ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA binding / magnesium ion binding / extracellular space / ATP binding / cytosol
Similarity search - Function
Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / 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
Chem-C6I / LYSINE / Lysine--tRNA ligase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsDawson, A. / Robinson, D.A. / Tamjar, J. / Wyatt, P. / Green, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1066891 United States
CitationJournal: Nat Commun / Year: 2022
Title: Lysyl-tRNA synthetase, a target for urgently needed M. tuberculosis drugs.
Authors: Green, S.R. / Davis, S.H. / Damerow, S. / Engelhart, C.A. / Mathieson, M. / Baragana, B. / Robinson, D.A. / Tamjar, J. / Dawson, A. / Tamaki, F.K. / Buchanan, K.I. / Post, J. / Dowers, K. / ...Authors: Green, S.R. / Davis, S.H. / Damerow, S. / Engelhart, C.A. / Mathieson, M. / Baragana, B. / Robinson, D.A. / Tamjar, J. / Dawson, A. / Tamaki, F.K. / Buchanan, K.I. / Post, J. / Dowers, K. / Shepherd, S.M. / Jansen, C. / Zuccotto, F. / Gilbert, I.H. / Epemolu, O. / Riley, J. / Stojanovski, L. / Osuna-Cabello, M. / Perez-Herran, E. / Rebollo, M.J. / Guijarro Lopez, L. / Casado Castro, P. / Camino, I. / Kim, H.C. / Bean, J.M. / Nahiyaan, N. / Rhee, K.Y. / Wang, Q. / Tan, V.Y. / Boshoff, H.I.M. / Converse, P.J. / Li, S.Y. / Chang, Y.S. / Fotouhi, N. / Upton, A.M. / Nuermberger, E.L. / Schnappinger, D. / Read, K.D. / Encinas, L. / Bates, R.H. / Wyatt, P.G. / Cleghorn, L.A.T.
History
DepositionDec 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Feb 7, 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
A: Lysine--tRNA ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5263
Polymers58,1301
Non-polymers3962
Water1,29772
1
A: Lysine--tRNA ligase 1
hetero molecules

A: Lysine--tRNA ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0526
Polymers116,2592
Non-polymers7934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area8410 Å2
ΔGint-31 kcal/mol
Surface area36880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.891, 82.891, 146.616
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-772-

HOH

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Components

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


Mass: 58129.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (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 / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-C6I / 6-azanyl-2-cyclohexyl-4-fluoranyl-1~{H}-pyrrolo[3,4-c]pyridin-3-one


Mass: 249.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C13H16FN3O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.16 Å3/Da / Density % sol: 43.16 % / Description: Block
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Reservoir: 0.25 M NaOAc and 14% w/v PEG 3350 Protein buffer:100 mM HEPES, 150 mM NaCl, 5% glycerol, pH 7.5 Protein conc ~20mg/ml
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: Jul 29, 2017
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.58→82.89 Å / Num. obs: 16758 / % possible obs: 99.9 % / Redundancy: 8.3 % / CC1/2: 1 / Rmerge(I) obs: 0.293 / Rpim(I) all: 0.109 / Net I/σ(I): 4.6
Reflection shellResolution: 2.58→2.62 Å / Redundancy: 8.8 % / Rmerge(I) obs: 3.027 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 797 / CC1/2: 0.709 / Rpim(I) all: 1.067 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5elo

5elo


Resolution: 2.58→72.26 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.882 / SU B: 28.305 / SU ML: 0.527 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.224 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3391 786 4.7 %RANDOM
Rwork0.2929 ---
obs0.2951 15842 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.9 Å2 / Biso mean: 59.863 Å2 / Biso min: 12.14 Å2
Baniso -1Baniso -2Baniso -3
1-3 Å2-0 Å2-0 Å2
2--3 Å20 Å2
3----6 Å2
Refinement stepCycle: final / Resolution: 2.58→72.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 0 18 72 3594
Biso mean--47.5 34.09 -
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133592
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173489
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.6574869
X-RAY DIFFRACTIONr_angle_other_deg1.1811.5877992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3495440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.11419.951203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.17115595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3321541
X-RAY DIFFRACTIONr_chiral_restr0.0520.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023996
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02838
LS refinement shellResolution: 2.58→2.647 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.642 62 -
Rwork0.458 1112 -
all-1174 -
obs--97.91 %

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