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- PDB-9tjw: Ternary complex of E. coli leucyl-tRNA synthetase mutant R178A, t... -

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Basic information

Entry
Database: PDB / ID: 9tjw
TitleTernary complex of E. coli leucyl-tRNA synthetase mutant R178A, tRNA(leu) and the leucyl adenylate analog LeuAMS in the aminoacyl transfer 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
5'-O-(L-leucylsulfamoyl)adenosine / : / RNA / RNA (> 10) / Leucine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.235 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)
C: Leucine--tRNA ligase
D: tRNA(leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,9087
Polymers254,9654
Non-polymers9433
Water12,430690
1
A: Leucine--tRNA ligase
B: tRNA(leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,9664
Polymers127,4832
Non-polymers4842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-54 kcal/mol
Surface area46490 Å2
MethodPISA
2
C: Leucine--tRNA ligase
D: tRNA(leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,9423
Polymers127,4832
Non-polymers4591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-44 kcal/mol
Surface area46410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.163, 68.89, 227.711
Angle α, β, γ (deg.)90, 104.61, 90
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 99429.898 Da / Num. of mol.: 2 / Mutation: R178A
Source method: isolated from a genetically manipulated source
Details: E. coli Leucyl tRNA synthetase with R178 mutation / 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.: 2
Source method: isolated from a genetically manipulated source
Details: E. coli tRNA(Leu) isoacceptor UAA / Source: (gene. exp.) Escherichia coli (E. coli)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
References: GenBank: 1231762938
#3: Chemical ChemComp-LSS / 5'-O-(L-leucylsulfamoyl)adenosine / 5-O-N-LEUCYL-SULFAMOYLADENOSINE


Mass: 459.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N7O7S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 690 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M BisTris pH5.5, 0.2M Ammonium Acetate, 23-26% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 7, 2024 / Details: Vertical CRL / Horizontal Eliptical mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.235→220.347 Å / Num. obs: 81602 / % possible obs: 89.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 38.4 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.094 / Rrim(I) all: 0.17 / Net I/σ(I): 5.5
Reflection shellResolution: 2.235→2.47 Å / Redundancy: 1.5 % / Rmerge(I) obs: 1.124 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4080 / CC1/2: 0.42 / Rpim(I) all: 0.716 / Rrim(I) all: 1.336 / % possible all: 41.1

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC20240123data reduction
STARANISOdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.235→220.35 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.607 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.66 / SU Rfree Blow DPI: 0.264 / SU Rfree Cruickshank DPI: 0.265
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 4139 -RANDOM
Rwork0.1932 77463 --
obs0.195 81602 70.7 %-
Displacement parametersBiso mean: 55.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.2232 Å20 Å21.7944 Å2
2---2.9706 Å20 Å2
3---1.7474 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.235→220.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13523 3350 63 690 17626
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00717645HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8424709HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5578SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2530HARMONIC5
X-RAY DIFFRACTIONt_it17645HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2398SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact12135SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion17.43
LS refinement shellResolution: 2.235→2.41 Å
RfactorNum. reflection% reflection
Rfree0.2871 96 -
Rwork0.2508 1537 -
obs--7.12 %
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)
11.14420.13290.35471.02380.04490.1631-0.0672-0.15320.16640.17590.03640.2696-0.0263-0.04080.0308-0.0553-0.0090.1082-0.06570.00620.0803-57.42378.8803-85.2717
20.15940.06830.04920.3364-0.14510.1390.0357-0.04190.03590.0591-0.02930.0245-0.00280.0096-0.0064-0.0005-0.02630.0497-0.0907-0.01580.0595-31.24618.8748-84.626
34.60040.1872-0.38160.4056-0.76250.7054-0.0973-0.7451-0.474-0.4872-0.0007-0.09180.4881-0.09020.0980.154-0.06460.03830.02650.1433-0.3382-69.177513.7127-28.2051
40.76180.38580.24630.3046-0.52550.98840.0073-0.15510.0654-0.0888-0.04610.01420.0890.02880.03880.00880.07190.04460.0486-0.0029-0.2342-52.09332.4861-29.5294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|* }B1 - 76
2X-RAY DIFFRACTION2{ A|* }A0 - 860
3X-RAY DIFFRACTION2{ A|* }A1001
4X-RAY DIFFRACTION3{ D|* }D1 - 76
5X-RAY DIFFRACTION4{ C|* }C1 - 860
6X-RAY DIFFRACTION4{ C|* }C901

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