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- PDB-7pqk: Co-Crystal Structure of M. tuberculosis LeuRS in Complex with the... -

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Basic information

Entry
Database: PDB / ID: 7pqk
TitleCo-Crystal Structure of M. tuberculosis LeuRS in Complex with the Adduct Formed by Prodrug Cmpd1 with Adenosine-monophosphate
ComponentsLeucine--tRNA ligase
KeywordsLIGASE / Leucyl-tRNA Synthetase / catalyses the reaction: ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) leucine-tRNA Ligase ATP binding domain
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / peptidoglycan-based cell wall / ATP binding / plasma membrane / cytosol
Similarity search - Function
Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site ...Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Chem-81D / Leucine--tRNA ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsPalencia, A. / Cusack, S.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)NovoTargetParasite France
Agence Nationale de la Recherche (ANR)AntibiOxaborole France
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Adenosine-Dependent Activation Mechanism of Prodrugs Targeting an Aminoacyl-tRNA Synthetase.
Authors: Hoffmann, G. / Le Gorrec, M. / Mestdach, E. / Cusack, S. / Salmon, L. / Jensen, M.R. / Palencia, A.
History
DepositionSep 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: 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
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

Downloads & links

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Assembly

Deposited unit
A: Leucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5693
Polymers24,9211
Non-polymers6482
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint2 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.170, 61.800, 77.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Leucine--tRNA ligase / Leucyl-tRNA synthetase / LeuRS


Mass: 24920.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Contain N-term His tag,
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: leuS, Rv0041, MTCY21D4.04 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFV1, leucine-tRNA ligase
#2: Chemical ChemComp-81D / (S)-3-(Aminomethyl)-4-chloro-7-(2-hydroxyethoxy)benzo[c][1,2]oxaborol-1(3H)-ol / [(1R,5S,6R,8R,9'S)-9'-(aminomethyl)-8-(6-aminopurin-9-yl)-2'-chloranyl-5'-(2-hydroxyethyloxy)spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,7'-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-triene]-6-yl]methyl dihydrogen phosphate


Mass: 585.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24BClN6O10P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: 3D-rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-TRIS (pH 5.5), 17% (w/v) PEG 10000 and 0.2 M ammonium acetate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0615 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2013
RadiationMonochromator: Silicon crystal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0615 Å / Relative weight: 1
ReflectionResolution: 1.15→38.595 Å / Num. obs: 74820 / % possible obs: 98.4 % / Redundancy: 4.887 % / Biso Wilson estimate: 14.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.058 / Χ2: 0.948 / Net I/σ(I): 9.16 / Num. measured all: 476869 / Scaling rejects: 165
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.15-1.264.441.1381.37175350.7811.1997.9
1.26-1.44.7860.4713.1153010.9340.53199.1
1.4-1.614.8840.1617.68141380.9880.18198.9
1.61-2.034.9210.06516.79137010.9970.07498.8
2.03-35.360.04627.7196220.9970.05199.7
3-58.730.04444.3734950.9980.04699.9
5-109.6430.04349.828910.9970.04699
10-158.8850.04752.61960.9950.05193.2
15-38.5957.220.06848.49410.9870.07189.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.27data extraction
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AGT

5agt


Resolution: 1.15→38.595 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 18.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1655 3758 5.02 %
Rwork0.1369 71029 -
obs0.1383 74787 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.7 Å2 / Biso mean: 23.43 Å2 / Biso min: 11.42 Å2
Refinement stepCycle: final / Resolution: 1.15→38.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1451 0 68 269 1788
Biso mean--22.27 38.31 -
Num. residues----195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021669
X-RAY DIFFRACTIONf_angle_d2.0292313
X-RAY DIFFRACTIONf_chiral_restr0.125253
X-RAY DIFFRACTIONf_plane_restr0.012307
X-RAY DIFFRACTIONf_dihedral_angle_d13.7631
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.15-1.16460.371280.3268258298
1.1646-1.17990.33731390.3099254198
1.1799-1.19610.28491300.2801260298
1.1961-1.21310.25691370.2726257398
1.2131-1.23130.27161410.2449256397
1.2313-1.25050.25191300.2222255197
1.2505-1.2710.23011480.2093261999
1.271-1.29290.25971310.2065261899
1.2929-1.31640.221370.1952261899
1.3164-1.34170.21691270.1832262899
1.3417-1.36910.21681330.1699260499
1.3691-1.39890.20371350.1517260199
1.3989-1.43150.18891290.1389261198
1.4315-1.46730.17611190.1286258397
1.4673-1.50690.14291620.11712636100
1.5069-1.55130.14351290.09962633100
1.5513-1.60130.13791450.09442628100
1.6013-1.65860.12781430.0917265499
1.6586-1.7250.13181480.0953262999
1.725-1.80350.15011450.0964263099
1.8035-1.89860.12871530.1019261398
1.8986-2.01750.11281620.1048260899
2.0175-2.17330.14291330.10412691100
2.1733-2.39190.13331450.1132684100
2.3919-2.7380.15691340.12762715100
2.738-3.44920.17891510.14012747100
3.4492-38.5950.17091440.1492286799

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