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- PDB-8pot: Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and ... -

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Basic information

Entry
Database: PDB / ID: 8pot
TitleTernary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and the benzoxaborole cmpd9 in the editing conformation
Components
  • Leucine--tRNA ligase
  • tRNA(leu)
KeywordsLIGASE / Leucine tRNA ligase / ATP binding protein / tRNA aminoacylation for protein translation / cytosolic Reaction catalysed: ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu)
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytosol
Similarity search - Function
Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / 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) ...Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / 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
: / RNA / RNA (> 10) / Leucine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.149 Å
AuthorsPalencia, A. / Hoffmann, G.
Funding support France, European Union, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-AMRB-0003-01 AntibiOxaborole France
Agence Nationale de la Recherche (ANR)ANR JCJC RC18114CC NovoTargetParasite France
iNEXT653706European Union
CitationJournal: Science Advances / Year: 2024
Title: Targeting A Microbiota Wolbachian Aminoacyl-tRNA Synthetase To Block Its Pathogenic Host
Authors: Palencia, A. / Hoffmann, G. / Lukarska, M. / Clare, R. / Ward, S. / Taylor, M.A. / Ringkjobing Jensen, M.
History
DepositionJul 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine--tRNA ligase
B: tRNA(leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4405
Polymers127,5692
Non-polymers8713
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-26 kcal/mol
Surface area47990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.167, 76.794, 90.863
Angle α, β, γ (deg.)90, 102.55, 90
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 99516.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: leuS, b0642, JW0637 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P07813, leucine-tRNA ligase
#2: RNA chain tRNA(leu)


Mass: 28052.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Obtained by T7 Pol in vitro transcription / Source: (synth.) Escherichia coli K-12 (bacteria)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-7RZ / [(1R,3'S,5S,6R,8R)-3'-(aminomethyl)-8-(6-aminopurin-9-yl)-4'-bromanyl-7'-[3-[methyl-(phenylmethyl)amino]propoxy]spiro[2,4,7-trioxa-3$l^{4}-borabicyclo[3.3.0]octane-3,1'-3H-2,1$l^{4}-benzoxaborole]-6-yl]methyl dihydrogen phosphate / AMP adduct with 3-[[(3S)-3-(aminomethyl)-4-bromanyl-1,3-dihydro-2,1-benzoxaborol-7-yl]oxy]-N-methyl-N-(phenylmethyl)propan-1-amine


Type: RNA OH 3 prime terminus / Mass: 747.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H35BBrN7O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.5 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium acetate pH5.6, 0.2 M NaCl, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.149→58.056 Å / Num. obs: 44722 / % possible obs: 91.2 % / Redundancy: 4.5 % / CC1/2: 0.962 / Rpim(I) all: 0.062 / Net I/σ(I): 7.1
Reflection shellResolution: 2.149→2.374 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2236 / CC1/2: 0.654 / Rpim(I) all: 0.503 / % possible all: 58.4

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC1.0.5data reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.149→58.06 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.893 / SU R Cruickshank DPI: 0.491 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.517 / SU Rfree Blow DPI: 0.284 / SU Rfree Cruickshank DPI: 0.284
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 2224 -RANDOM
Rwork0.2139 ---
obs0.2166 44722 68.3 %-
Displacement parametersBiso mean: 53.24 Å2
Baniso -1Baniso -2Baniso -3
1-1.2163 Å20 Å2-0.5139 Å2
2---0.3852 Å20 Å2
3----0.831 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.149→58.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6496 1795 55 377 8723
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0078738HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8512264HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2743SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1236HARMONIC5
X-RAY DIFFRACTIONt_it8738HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1189SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6344SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion17.57
LS refinement shellResolution: 2.15→2.31 Å
RfactorNum. reflection% reflection
Rfree0.3112 37 -
Rwork0.2733 --
obs0.2749 895 7.15 %

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