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- PDB-8h9a: Crystal structure of chemically modified E. coli ThrS catalytic d... -

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Basic information

Entry
Database: PDB / ID: 8h9a
TitleCrystal structure of chemically modified E. coli ThrS catalytic domain 2
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 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: 1.9 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 1.2Nov 13, 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

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Assembly

Deposited unit
A: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3353
Polymers47,8941
Non-polymers4422
Water5,495305
1
A: Threonine--tRNA ligase
hetero molecules

A: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6716
Polymers95,7872
Non-polymers8834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4120 Å2
ΔGint-19 kcal/mol
Surface area32970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.620, 91.620, 121.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 47893.523 Da / Num. of mol.: 1 / Fragment: UNP residues 242-642 / Mutation: Y462K
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
#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.: 1
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.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2.0 M smmonium sulfate, 0.15 M sodium citrate, pH 5.5

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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: 1.89→50 Å / Num. obs: 25514 / % possible obs: 98.1 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.1
Reflection shellResolution: 1.89→1.94 Å / Rmerge(I) obs: 0.606 / Num. unique obs: 2980

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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: 1.9→42.87 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 1305 5.11 %
Rwork0.1809 24209 -
obs0.1835 25514 53.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.36 Å2 / Biso mean: 28.9811 Å2 / Biso min: 7.37 Å2
Refinement stepCycle: final / Resolution: 1.9→42.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3239 0 1 305 3545
Biso mean--18.1 33.93 -
Num. residues----399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.970.5473130.34221361493
1.97-2.060.2596100.24494424529
2.06-2.170.2537490.222177282116
2.17-2.310.3207610.2891275133626
2.31-2.480.23541140.21642180229444
2.48-2.730.27182480.21384155440384
2.73-3.130.26492730.204449935266100
3.13-3.940.23552400.163350785318100
3.94-42.870.18732970.15135178547599

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