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- PDB-8h9c: Crystal structure of chemically modified E. coli ThrS catalytic d... -

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Basic information

Entry
Database: PDB / ID: 8h9c
TitleCrystal structure of chemically modified E. coli ThrS catalytic domain 4
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 / TGS-like / TGS domain profile. ...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 / 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 / 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: 2.15 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 20, 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)48,3633
Polymers47,9221
Non-polymers4422
Water3,405189
1
A: Threonine--tRNA ligase
hetero molecules

A: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7276
Polymers95,8432
Non-polymers8834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4070 Å2
ΔGint-20 kcal/mol
Surface area33280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.180, 92.180, 120.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-931-

HOH

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Components

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


Mass: 47921.535 Da / Num. of mol.: 1 / Fragment: UNP residues 242-642 / Mutation: Y462R
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.: 189 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.02 M DL-glutamic acid monohydrate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine monohydrochloride, 0.02 M DL-serine, 0.05 M sodium HEPES, 0.05 M MOPS (acid), pH 7.5, 20% v/v ...Details: 0.02 M DL-glutamic acid monohydrate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine monohydrochloride, 0.02 M DL-serine, 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: 0.97856 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: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 12955 / % possible obs: 100 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10
Reflection shellResolution: 2.14→2.2 Å / Rmerge(I) obs: 0.778 / Num. unique obs: 2446

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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: 2.15→48.14 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.31 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2756 622 4.8 %
Rwork0.2255 12333 -
obs0.2278 12955 39.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 37.95 Å2 / Biso mean: 18.7157 Å2 / Biso min: 8.68 Å2
Refinement stepCycle: final / Resolution: 2.15→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3265 0 0 189 3454
Biso mean---16.17 -
Num. residues----399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.370.3015110.36942983094
2.37-2.710.3698620.3031041110314
2.71-3.410.3551640.26773089325340
3.41-48.140.24023850.20247905829098
Refinement TLS params.Method: refined / Origin x: 41.9046 Å / Origin y: 1.374 Å / Origin z: 8.1045 Å
111213212223313233
T0.1042 Å2-0.0518 Å2-0.0215 Å2-0.1535 Å20.0093 Å2---0.0342 Å2
L0.2215 °20.1479 °2-0.0827 °2-0.6747 °20.1801 °2--1.0919 °2
S0.0083 Å °0.0059 Å °0.0311 Å °-0.0215 Å °0.0735 Å °0.0335 Å °-0.0666 Å °-0.0544 Å °0.0437 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA242 - 640
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 203

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