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- PDB-8h99: Crystal structure of E. coli ThrS catalytic domain mutant -

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Basic information

Entry
Database: PDB / ID: 8h99
TitleCrystal structure of E. coli ThrS catalytic domain mutant
ComponentsThreonine--tRNA ligase
KeywordsLIGASE / Threonine--tRNA ligase
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/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS ...Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / TGS-like / 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 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Beta-grasp domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / IMIDAZOLE / Threonine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,20412
Polymers95,8232
Non-polymers1,38110
Water12,574698
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-122 kcal/mol
Surface area31500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.730, 109.990, 114.700
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 AB

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


Mass: 47911.516 Da / Num. of mol.: 2 / Fragment: UNP residues 242-642 / Mutation: Y462F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: E2QMS9, threonine-tRNA ligase

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Non-polymers , 5 types, 708 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 698 / 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: 2.85 Å3/Da / Density % sol: 56.91 %
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, 0.045 M imidazole, 0.055 M MES monohydrate (acid), pH 6.5, 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: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 79665 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.9
Reflection shellResolution: 1.94→1.99 Å / Rmerge(I) obs: 0.91 / Num. unique obs: 5962

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FYF

1fyf


Resolution: 1.94→40.56 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 3957 4.97 %
Rwork0.177 --
obs0.178 79665 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.13 Å2
Refinement stepCycle: LAST / Resolution: 1.94→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6463 0 78 698 7239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.010.27183240.23775716X-RAY DIFFRACTION75
2.01-2.090.26613940.22847652X-RAY DIFFRACTION100
2.09-2.180.21853800.19377711X-RAY DIFFRACTION100
2.18-2.30.22394200.19027671X-RAY DIFFRACTION100
2.3-2.440.22433900.1827753X-RAY DIFFRACTION100
2.44-2.630.20583720.17897743X-RAY DIFFRACTION100
2.63-2.90.22143980.18147758X-RAY DIFFRACTION100
2.9-3.320.19613850.17687804X-RAY DIFFRACTION100
3.32-4.180.17984310.15597825X-RAY DIFFRACTION100
4.18-40.560.17294630.16128075X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -23.5372 Å / Origin y: 22.0606 Å / Origin z: -24.2471 Å
111213212223313233
T0.1114 Å20.0154 Å2-0.0039 Å2-0.0987 Å2-0.0058 Å2--0.0929 Å2
L0.7001 °20.0476 °20.1336 °2-0.783 °2-0.1213 °2--0.5208 °2
S0.0322 Å °0.0038 Å °-0.0128 Å °-0.0926 Å °-0.031 Å °0.0216 Å °0.0035 Å °0.0017 Å °-0.0019 Å °
Refinement TLS groupSelection details: ALL

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