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- PDB-9tjt: Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and ... -

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Basic information

Entry
Database: PDB / ID: 9tjt
TitleTernary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and the benzoxaborole cmpd6 in the pre-activation state
Components
  • Leucine--tRNA ligase
  • tRNA(leu)
KeywordsRNA BINDING PROTEIN / Leucine tRNA ligase Antimicrobial target tRNA aminoacylation for protein translation
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA deacylase 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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsHoffmann, G. / Palencia, A.
Funding support France, European Union, 4items
OrganizationGrant numberCountry
Grenoble Instruct-ERIC Center (ISBG)27604 France
iNEXT-Discovery45625European Union
Agence Nationale de la Recherche (ANR)ANR-20-AMRB-0003 France
Agence Nationale de la Recherche (ANR)ANR-22-CE44-0040 France
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: The Zn Domain Acts as a Dynamic Switch Coordinating Multiple-Step Aminoacylation in Bacterial Leucyl-tRNA Synthetase
Authors: Hoffmann, G. / Dulic, M. / Gruic-Sovulj, I. / Palencia, A.
History
DepositionDec 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)128,1375
Polymers127,2392
Non-polymers8983
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-34 kcal/mol
Surface area48020 Å2
Unit cell
Length a, b, c (Å)89.23, 77.19, 90.82
Angle α, β, γ (deg.)90, 102.58, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

#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
Details: E. coli Leucyl tRNA synthetase / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: leuS, b0642, JW0637 / Production host: Escherichia coli (E. coli) / References: UniProt: P07813, leucine-tRNA ligase
#2: RNA chain tRNA(leu)


Mass: 27723.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: E. coli tRNA(Leu) isoacceptor UAA with cmpd6 covalently bound to Adenosine 76
Source: (gene. exp.) Escherichia coli (E. coli)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
References: GenBank: 1845258627

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Non-polymers , 4 types, 103 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EYT / [(1~{R},5~{S},6~{R},8~{R},9'~{S})-9'-(aminomethyl)-8-(6-aminopurin-9-yl)-2'-bromanyl-5'-[3-oxidanylidene-3-(1,3-thiazol-2-ylamino)propoxy]spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,7'-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-6-yl]methyl dihydrogen phosphate


Mass: 740.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26BBrN8O10PS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.73 %
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: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.87→88.64 Å / Num. obs: 27637 / % possible obs: 99.4 % / Redundancy: 3.98 % / Biso Wilson estimate: 56 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.14 / Net I/σ(I): 9.63
Reflection shellResolution: 2.87→2.94 Å / Mean I/σ(I) obs: 1.96 / Num. unique obs: 1909 / CC1/2: 0.64 / Rrim(I) all: 0.82

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→45.48 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.386
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 1380 -RANDOM
Rwork0.2039 26257 --
obs0.2061 27637 99.5 %-
Displacement parametersBiso mean: 67.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.0562 Å20 Å212.8894 Å2
2--4.7712 Å20 Å2
3----2.7149 Å2
Refine analyzeLuzzati coordinate error obs: 0.366 Å
Refinement stepCycle: LAST / Resolution: 2.87→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6705 1737 52 100 8594
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0068860HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7912424HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2784SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1270HARMONIC5
X-RAY DIFFRACTIONt_it8860HARMONIC10
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion1203SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5928SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion18.27
LS refinement shellResolution: 2.87→2.89 Å
RfactorNum. reflection% reflection
Rfree0.328 23 -
Rwork0.2838 530 -
obs0.2856 553 99.47 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6935-1.76782.01271.7143-0.71261.1050.16250.2462-0.4722-0.27650.05780.17370.2434-0.1689-0.2203-0.0563-0.0722-0.0643-0.0754-0.0413-0.1581-6.6567-7.4828106.4989
20.3266-0.20220.28720.3298-0.21890.53380.02390.0780.01770.0142-0.0571-0.01880.0093-0.01690.0332-0.0008-0.0205-0.0107-0.1157-0.0166-0.024419.41563.3757110.1071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|* }B1 - 75
2X-RAY DIFFRACTION1{ B|* }B76
3X-RAY DIFFRACTION2{ A|* }A1 - 860
4X-RAY DIFFRACTION2{ A|* }A900

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