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- PDB-9twv: Complex of E. coli leucyl-tRNA synthetase AN3365-resistant mutant... -

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Basic information

Entry
Database: PDB / ID: 9twv
TitleComplex of E. coli leucyl-tRNA synthetase AN3365-resistant mutant D345A bound to tRNA(leu)
Components
  • Leucine--tRNA ligase
  • tRNA(leu)
KeywordsRNA BINDING PROTEIN / Leucine tRNA ligase Antimicrobial target resistant mutant Epetraborole
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
: / DI(HYDROXYETHYL)ETHER / : / RNA / RNA (> 10) / Leucine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.111 Å
AuthorsHoffmann, G. / Palencia, A. / Muller, B.
Funding supportEuropean Union, France, 4items
OrganizationGrant numberCountry
iNEXT-Discovery45625European Union
Grenoble Instruct-ERIC Center (ISBG)27604 France
Agence Nationale de la Recherche (ANR)ANR-20-AMRB-0003 France
Agence Nationale de la Recherche (ANR)ANR-22-CE44-0040 France
CitationJournal: Nat Commun / Year: 2026
Title: Mechanisms of Resistance to an Antibiotic Targeting Bacterial Leucyl-tRNA Synthetase
Authors: Muller, B. / Fries, F. / Huber, A.L. / Risch, T. / Mohamadyar-Toupkanlou, F. / Hoffmann, G. / Dulic, M. / Herrmann, J. / Guic Sovulj, I. / Muller, R. / Palencia, A.
History
DepositionJan 15, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: 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)127,9425
Polymers127,5252
Non-polymers4183
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-47 kcal/mol
Surface area45870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.799, 118.955, 140.713
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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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: 99472.008 Da / Num. of mol.: 1 / Mutation: D345A
Source method: isolated from a genetically manipulated source
Details: E. coli Leucyl tRNA synthetase D345A mutant / 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: 28052.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: E. coli tRNA(Leu) isoacceptor UAA / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1231762938

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Non-polymers , 4 types, 468 molecules

#3: Chemical ChemComp-A1JX6 / (2~{S})-2-azanyl-~{N}-[azanyl-(3-fluorophenyl)-oxidanylidene-$l^{6}-sulfanylidene]-4-methyl-pentanamide


Mass: 287.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18FN3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M KH2PO4, 19-23% PEG 3350

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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 2M / Detector: PIXEL / Date: Mar 12, 2022 / Details: Vertical CRL / Horizontal CRL
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.11→60.56 Å / Num. obs: 66174 / % possible obs: 95.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 47.5 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.029 / Net I/σ(I): 14.8
Reflection shellResolution: 2.11→2.23 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3309 / CC1/2: 0.619 / Rpim(I) all: 0.492 / % possible all: 61.6

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.111→60.56 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.261 / SU Rfree Blow DPI: 0.203 / SU Rfree Cruickshank DPI: 0.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 3254 -RANDOM
Rwork0.2149 62920 --
obs0.2167 66174 88.5 %-
Displacement parametersBiso mean: 63.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.6295 Å20 Å20 Å2
2--0.7085 Å20 Å2
3----0.079 Å2
Refine analyzeLuzzati coordinate error obs: 0.292 Å
Refinement stepCycle: LAST / Resolution: 2.111→60.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6457 1731 27 465 8680
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088595HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8212058HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2694SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1222HARMONIC5
X-RAY DIFFRACTIONt_it8595HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1169SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6456SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion17.24
LS refinement shellResolution: 2.111→2.18 Å
RfactorNum. reflection% reflection
Rfree0.3039 65 -
Rwork0.2739 1259 -
obs--18.3 %
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)
10.5212-0.067-0.37022.1173-0.94570.01360.17470.1623-0.0353-0.2075-0.5321-0.3582-0.15560.45850.35740.049-0.03420.03730.14930.1443-0.069610.5192-6.248.2611
20.09990.03920.0640.36530.06670.2757-0.05910.00080.0529-0.11650.03730.0006-0.02410.01620.0217-0.04550.03340.0257-0.00340.0156-0.0130.094217.285319.0285
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|* }B1 - 76
2X-RAY DIFFRACTION2{ A|* }A0 - 859
3X-RAY DIFFRACTION2{ A|* }A901 - 902

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