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- PDB-8por: Crystal structure of wolbachia leucyl-tRNA synthetase editing dom... -

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Basic information

Entry
Database: PDB / ID: 8por
TitleCrystal structure of wolbachia leucyl-tRNA synthetase editing domain bound to cmpd6-AMP adduct
ComponentsLeucine--tRNA ligase
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
: / Leucine--tRNA ligase
Similarity search - Component
Biological speciesWolbachia endosymbiont strain TRS of Brugia malayi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPalencia, A. / Lukarska, M.
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2655
Polymers20,0121
Non-polymers1,2534
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, elution volume suggests monomer, isothermal titration calorimetry, protein molecule (chain A) binds to 1 adduct cmpd6-AMP
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-4 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.630, 126.630, 61.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-593-

HOH

21A-625-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 20012.182 Da / Num. of mol.: 1 / Mutation: deletion 354-477
Source method: isolated from a genetically manipulated source
Details: residue 30 (cysteine 243) is a S-mercaptocysteine (denoted CSS in PDB entries)
Source: (gene. exp.) Wolbachia endosymbiont strain TRS of Brugia malayi (bacteria)
Gene: leuS, Wbm0605 / Plasmid: pET-M11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q5GS31, leucine-tRNA ligase

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Non-polymers , 5 types, 138 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.56 Å3/Da / Density % sol: 65.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5; 0.2M LiSO4; 31% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97924 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.85→109.66 Å / Num. obs: 24048 / % possible obs: 100 % / Redundancy: 16.2 % / CC1/2: 1 / Rrim(I) all: 0.09 / Net I/σ(I): 21.91
Reflection shellResolution: 1.85→1.93 Å / Redundancy: 16.8 % / Mean I/σ(I) obs: 1.62 / Num. unique obs: 1281 / CC1/2: 0.67 / Rrim(I) all: 1.89 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→44.19 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.975 / SU B: 6.577 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16602 1281 5.1 %RANDOM
Rwork0.1471 ---
obs0.14812 24048 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.348 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å2-1.03 Å20 Å2
2---2.06 Å20 Å2
3---6.68 Å2
Refinement stepCycle: 1 / Resolution: 1.85→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1293 0 77 134 1504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131433
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171366
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.7061943
X-RAY DIFFRACTIONr_angle_other_deg1.2961.6283192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.165174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.6192562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42115252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.181153
X-RAY DIFFRACTIONr_chiral_restr0.2190.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021519
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02257
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8324.532666
X-RAY DIFFRACTIONr_mcbond_other3.82615.944665
X-RAY DIFFRACTIONr_mcangle_it5.143832
X-RAY DIFFRACTIONr_mcangle_other5.169833
X-RAY DIFFRACTIONr_scbond_it5.0753.958766
X-RAY DIFFRACTIONr_scbond_other5.072767
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.43145.9911106
X-RAY DIFFRACTIONr_long_range_B_refined7.6921528
X-RAY DIFFRACTIONr_long_range_B_other7.5761507
X-RAY DIFFRACTIONr_rigid_bond_restr3.05531427
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 115 -
Rwork0.303 1717 -
obs--100 %

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