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- PDB-8h98: Crystal structure of chemically modified E. coli ThrS catalytic d... -

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Basic information

Entry
Database: PDB / ID: 8h98
TitleCrystal structure of chemically modified E. coli ThrS catalytic domain 1
ComponentsThreonine--tRNA ligase
KeywordsLIGASE / Threonine--tRNA ligase
Function / homology
Function and homology information


aminoacyl-tRNA ligase activity / tRNA aminoacylation / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA deacylase activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding ...aminoacyl-tRNA ligase activity / tRNA aminoacylation / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA aminoacylation for protein translation / aminoacyl-tRNA deacylase activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding / regulation of translation / tRNA binding / response to antibiotic / protein homodimerization activity / RNA binding / zinc ion binding / ATP binding / cytoplasm / 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-X5V / Threonine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsQiao, H. / Xia, M. / Wang, J. / Fang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21977107 China
CitationJournal: Commun Biol / Year: 2023
Title: Tyrosine-targeted covalent inhibition of a tRNA synthetase aided by zinc ion.
Authors: Qiao, H. / Xia, M. / Cheng, Y. / Zhou, J. / Zheng, L. / Li, W. / Wang, J. / Fang, P.
History
DepositionOct 25, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,7386
Polymers95,8552
Non-polymers8834
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-18 kcal/mol
Surface area32810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.750, 105.910, 134.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 47927.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: thrS, b1719, JW1709 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8M3, threonine-tRNA ligase
#2: Chemical ChemComp-X5V / N-(2,3-dihydroxybenzoyl)-4-(4-nitrophenyl)-L-threonine


Type: L-peptide NH3 amino terminus / Mass: 376.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C17H16N2O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.64 Å3/Da / Density % sol: 66.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.03 M diethylene glycol, 0.03 M triethylene glycol, 0.03 M tetraehylene glycol, 0.03 M pentaethylene glycol, 0.05 M sodium HEPES, 0.05 M MOPS (acid), pH 7.5, 20% v/v ethylene glycol, 10% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 36908 / % possible obs: 97 % / Redundancy: 4.4 % / Biso Wilson estimate: 41.78 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.4
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 1.03 / Num. unique obs: 1021

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FYF

1fyf


Resolution: 2.5→49.28 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 29.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2303 1875 5.08 %
Rwork0.1911 35033 -
obs0.1931 36908 75.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.12 Å2 / Biso mean: 48.1872 Å2 / Biso min: 25.8 Å2
Refinement stepCycle: final / Resolution: 2.5→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6539 0 2 274 6815
Biso mean--36.13 45.44 -
Num. residues----800
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.590.3008570.26961021107822
2.59-2.690.28981000.25071877197741
2.69-2.820.30251430.26622584272756
2.82-2.960.30781590.27373262342171
2.96-3.150.29472110.24863915412685
3.15-3.390.26962190.22844481470096
3.39-3.730.24942400.19254465470596
3.73-4.270.21322540.16224475472996
4.27-5.380.19022510.14824456470795
5.38-49.280.18732410.16894497473892
Refinement TLS params.Method: refined / Origin x: 14.2689 Å / Origin y: 26.5611 Å / Origin z: 37.1201 Å
111213212223313233
T0.2848 Å20.0331 Å20.0354 Å2-0.2779 Å20.0778 Å2--0.2379 Å2
L1.1536 °20.1648 °20.0179 °2-1.3123 °2-0.062 °2--0.6253 °2
S0.1582 Å °0.0328 Å °0.1049 Å °-0.1396 Å °-0.1989 Å °-0.066 Å °0.0036 Å °0.035 Å °0.0371 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB242 - 641
2X-RAY DIFFRACTION1allA242 - 641
3X-RAY DIFFRACTION1allD1 - 2
4X-RAY DIFFRACTION1allS1 - 341

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