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- PDB-8ou8: Crystal structure of E. coli threonyl tRNA synthetase in complex ... -

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Basic information

Entry
Database: PDB / ID: 8ou8
TitleCrystal structure of E. coli threonyl tRNA synthetase in complex with a TM84 analogue
ComponentsThreonine--tRNA ligase
KeywordsRNA BINDING PROTEIN / threonyl tRNA synthetase / e. coli / inhibitor / complex
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 / : / TGS domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / TGS-like ...Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / TGS-like / tRNA synthetase class II core domain (G, H, P, S and T) / TGS domain profile. / TGS / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / 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)
Similarity search - Domain/homology
Chem-W0U / Threonine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli IAI1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsRodriguez Buitrago, J.A. / Parisini, E. / Aigars, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.1/19/A/019European Union
CitationJournal: Org.Biomol.Chem. / Year: 2023
Title: Synthesis and evaluation of an agrocin 84 toxic moiety (TM84) analogue as a malarial threonyl tRNA synthetase inhibitor.
Authors: Buitrago, J.A.R. / Leitis, G. / Kanepe-Lapsa, I. / Rudnickiha, A. / Parisini, E. / Jirgensons, A.
History
DepositionApr 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Sep 6, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_planes
Item: _pdbx_validate_planes.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,27110
Polymers95,9972
Non-polymers1,2748
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-4 kcal/mol
Surface area30930 Å2
Unit cell
Length a, b, c (Å)85.330, 108.950, 113.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules DA

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


Mass: 47998.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: LIG DMS EDO / Source: (gene. exp.) Escherichia coli IAI1 (bacteria) / Gene: thrS, ECIAI1_1775 / Plasmid: pET-28a(+) / Details (production host): NcoI(CCATGG), HindIII(AAGCTT) / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): BL21DE3 / References: UniProt: B7M1C7, threonine-tRNA ligase

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Non-polymers , 5 types, 225 molecules

#2: Chemical ChemComp-W0U / [(2~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methoxy-~{N}-[(2~{S},3~{S})-2-azanyl-3-oxidanyl-butanoyl]phosphonamidic acid


Mass: 431.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H22N7O7P
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.763131 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 12% (w/v) PEG 4000, 21% (v/v) MPD, and 0.1 M sodium citrate
PH range: 5.0 - 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jun 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→78.75 Å / Num. obs: 45827 / % possible obs: 99 % / Redundancy: 2.2 % / CC1/2: 0.994 / Net I/σ(I): 9.3
Reflection shellResolution: 2.05→2.258 Å / Num. unique obs: 485405 / CC1/2: 0.996 / % possible all: 48

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Processing

Software
NameVersionClassification
autoPROC5.8.0352data processing
xia2.multiplexv1.0data reduction
Aimlessv1.0data scaling
PHASERv1.0phasing
REFMACV1.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→78.75 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.606 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2397 5.2 %RANDOM
Rwork0.18892 ---
obs0.216 43429 68.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.717 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å2-0 Å20 Å2
2--0.18 Å2-0 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 2.05→78.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 39 217 6816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126755
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166070
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.6469097
X-RAY DIFFRACTIONr_angle_other_deg0.5221.55614167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7755799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.0561062
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.127101221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2954
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027706
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021396
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_it3.5114.1833196
X-RAY DIFFRACTIONr_mcbond_other3.5114.1823196
X-RAY DIFFRACTIONr_mcangle_it4.9276.2753992
X-RAY DIFFRACTIONr_mcangle_other4.9266.2783993
X-RAY DIFFRACTIONr_scbond_it4.4194.5653559
X-RAY DIFFRACTIONr_scbond_other4.4184.5663560
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4246.675105
X-RAY DIFFRACTIONr_long_range_B_refined8.62552.5187679
X-RAY DIFFRACTIONr_long_range_B_other8.58952.4997661
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.051→2.104 Å
RfactorNum. reflection% reflection
Rfree0.286 8 -
Rwork0.259 170 -
obs--36.2 %

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