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- PDB-8wia: Crystal structure of E. coli ThrS catalytic domain mutant G463S -

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Basic information

Entry
Database: PDB / ID: 8wia
TitleCrystal structure of E. coli ThrS catalytic domain mutant G463S
ComponentsThreonine--tRNA ligase
KeywordsLIGASE / Threonine--tRNA ligase
Function / homology:
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsQiao, H. / Wang, Z. / Wang, J. / Fang, P.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2022YFC2303100 China
CitationJournal: Commun Biol / Year: 2024
Title: Specific glycine-dependent enzyme motion determines the potency of conformation selective inhibitors of threonyl-tRNA synthetase.
Authors: Qiao, H. / Wang, Z. / Yang, H. / Xia, M. / Yang, G. / Bai, F. / Wang, J. / Fang, P.
History
DepositionSep 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Author supporting evidence / Structure summary / Category: pdbx_audit_support / pdbx_entry_details
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _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
B: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0464
Polymers95,9152
Non-polymers1312
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-94 kcal/mol
Surface area33310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.964, 107.408, 112.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Threonine--tRNA ligase


Mass: 47957.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: thrS / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8S7FUD7
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate tribasic, 0.02 M potassium sodium tartrate tetrahydrate, 0.02 M sodium oxamate, 0.045 M imidazole, 0.055 M MES ...Details: 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate tribasic, 0.02 M potassium sodium tartrate tetrahydrate, 0.02 M sodium oxamate, 0.045 M imidazole, 0.055 M MES monohydrate acid pH 6.5, 20% v/v PEG 500 MME, 10% w/v PEG 20000

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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: Jan 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.96→77.78 Å / Num. obs: 77887 / % possible obs: 97.2 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.035 / Rrim(I) all: 0.096 / Χ2: 0.93 / Net I/σ(I): 12.9 / Num. measured all: 566037
Reflection shellResolution: 1.96→2.06 Å / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.922 / Num. measured all: 86590 / Num. unique obs: 11562 / CC1/2: 0.821 / Rpim(I) all: 0.356 / Rrim(I) all: 0.99 / Χ2: 0.83 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→42.18 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 3843 4.94 %
Rwork0.2122 --
obs0.2135 77734 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6529 0 2 574 7105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026696
X-RAY DIFFRACTIONf_angle_d0.4819021
X-RAY DIFFRACTIONf_dihedral_angle_d4.664894
X-RAY DIFFRACTIONf_chiral_restr0.042943
X-RAY DIFFRACTIONf_plane_restr0.0041181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.030.32053870.29697533X-RAY DIFFRACTION100
2.03-2.110.30724070.27637458X-RAY DIFFRACTION100
2.11-2.210.26493880.25237515X-RAY DIFFRACTION100
2.21-2.320.26642890.25025462X-RAY DIFFRACTION73
2.32-2.470.24973830.24557581X-RAY DIFFRACTION100
2.47-2.660.24724210.23867541X-RAY DIFFRACTION100
2.66-2.920.25873880.22947585X-RAY DIFFRACTION100
2.92-3.350.22963870.21227646X-RAY DIFFRACTION100
3.35-4.220.20723690.17957717X-RAY DIFFRACTION100
4.22-42.180.22564240.19217853X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -24.7703 Å / Origin y: 21.7114 Å / Origin z: -23.6761 Å
111213212223313233
T0.2803 Å20.006 Å2-0.0127 Å2-0.3079 Å20.0059 Å2--0.2686 Å2
L0.2532 °20.1025 °2-0.0038 °2-0.8318 °2-0.0743 °2--0.1885 °2
S0.0297 Å °-0.0141 Å °-0.018 Å °0.0895 Å °-0.0286 Å °0.0294 Å °-0.0274 Å °0.0083 Å °-0.0064 Å °
Refinement TLS groupSelection details: all

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