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- PDB-6l2p: Threonyl-tRNA synthetase from Salmonella enterica in the apo form -

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Basic information

Entry
Database: PDB / ID: 6l2p
TitleThreonyl-tRNA synthetase from Salmonella enterica in the apo form
ComponentsThreonine--tRNA ligase
KeywordsLIGASE / tRNA synthetase / drug target / homodimer
Function / homology
Function and homology information


threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / Threonyl/alanyl tRNA synthetase, SAD / TGS domain / Threonyl and Alanyl tRNA synthetase second additional domain / Anticodon-binding domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS-like ...Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / Threonyl/alanyl tRNA synthetase, SAD / TGS domain / Threonyl and Alanyl tRNA synthetase second additional domain / Anticodon-binding domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS-like / TGS domain profile. / TGS / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Beta-grasp domain superfamily / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Threonine--tRNA ligase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Cubana str. 76814 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGuo, J. / Chen, B. / Zhou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)81773636 China
CitationJournal: Eur.J.Med.Chem. / Year: 2019
Title: Discovery of novel tRNA-amino acid dual-site inhibitors against threonyl-tRNA synthetase by fragment-based target hopping.
Authors: Guo, J. / Chen, B. / Yu, Y. / Cheng, B. / Cheng, Y. / Ju, Y. / Gu, Q. / Xu, J. / Zhou, H.
History
DepositionOct 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Threonine--tRNA ligase
B: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0604
Polymers95,9292
Non-polymers1312
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-96 kcal/mol
Surface area33290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.988, 101.859, 106.047
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Threonine--tRNA ligase / Threonyl-tRNA synthetase / ThrRS


Mass: 47964.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Cubana str. 76814 (bacteria)
Gene: thrS, A628_05061 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: V7II86, threonine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.22 M lithium acetate pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 40001 / % possible obs: 97.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.049 / Rrim(I) all: 0.121 / Net I/σ(I): 22.035
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.49 / Num. unique obs: 1976 / CC1/2: 0.911 / Χ2: 0.557 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HWP

4hwp


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 19.159 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.396 / ESU R Free: 0.258
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 2065 5.2 %RANDOM
Rwork0.2205 ---
obs0.2227 37882 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 157.79 Å2 / Biso mean: 51.017 Å2 / Biso min: 24.07 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å20 Å2
2---1.17 Å2-0 Å2
3----1.94 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6480 0 2 126 6608
Biso mean--40.78 38.5 -
Num. residues----801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196622
X-RAY DIFFRACTIONr_bond_other_d0.0060.026208
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9458935
X-RAY DIFFRACTIONr_angle_other_deg0.875314230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4885799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53423.487347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.005151165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9751562
X-RAY DIFFRACTIONr_chiral_restr0.0590.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027557
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021629
LS refinement shellResolution: 2.301→2.361 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 150 -
Rwork0.292 2583 -
all-2733 -
obs--91.68 %
Refinement TLS params.

Method: refined / 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)
10.12690.1879-0.12360.4536-0.00460.43970.01140.04990.0187-0.07390.0306-0.0036-0.0536-0.0595-0.04210.4680.0251-0.02120.03870.01190.0672-0.8591.72910.806
21.11411.43280.43571.94530.28451.0384-0.0470.1128-0.0189-0.10220.1369-0.0240.03230.0444-0.08990.43510.01890.03750.02720.00680.052810.8544.82-1.224
30.75240.9397-0.08443.4461-0.40490.6004-0.0643-0.0205-0.0052-0.26680.06140.05980.11410.02610.0030.4175-0.0072-0.03260.0209-0.00580.0418-5.391-33.1643.608
40.35730.30340.18580.41260.1390.88880.03860.01280.0590.1003-0.04960.05740.0144-0.08840.0110.4222-0.00160.00310.03780.00370.0843-10.036-4.82424.015
51.45670.4603-0.00090.30360.02780.6664-0.1250.024-0.00180.17080.01510.0976-0.023-0.10070.10990.49220.01530.05810.0164-0.00930.0948-14.828-14.55735.009
64.42681.9321.14941.33330.93733.3119-0.16680.6094-0.56910.17620.359-0.1456-0.07180.8111-0.19220.34430.00820.00640.2324-0.10260.134824.943-16.92726.494
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A242 - 392
2X-RAY DIFFRACTION2A393 - 528
3X-RAY DIFFRACTION3A529 - 642
4X-RAY DIFFRACTION4B241 - 392
5X-RAY DIFFRACTION5B393 - 541
6X-RAY DIFFRACTION6B542 - 640

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