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- PDB-8wih: Crystal structure of E. coli ThrS catalytic domain mutant G463A i... -

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Basic information

Entry
Database: PDB / ID: 8wih
TitleCrystal structure of E. coli ThrS catalytic domain mutant G463A in complex with ATP
ComponentsThreonine--tRNA ligase
KeywordsLIGASE / Threonine--tRNA ligase
Function / homologyADENOSINE-5'-TRIPHOSPHATE / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 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)97,0286
Polymers95,8832
Non-polymers1,1454
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-94 kcal/mol
Surface area32230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.175, 109.376, 113.793
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 / Threonyl-tRNA synthetase / ThrRS


Mass: 47941.543 Da / Num. of mol.: 2 / Mutation: G463A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: thrS, CX696_002870 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8S7FUD7, threonine-tRNA ligase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#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.: 48 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 0.045 M imidazole, 0.055 M MES monohydrate acid pH 6.5, 20% v/v glycerol, 10% w/v PEG 4000

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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: Jun 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.44→78.86 Å / Num. obs: 36771 / % possible obs: 88.7 % / Redundancy: 8.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.039 / Rrim(I) all: 0.12 / Χ2: 0.97 / Net I/σ(I): 14.2 / Num. measured all: 325461
Reflection shellResolution: 2.44→2.57 Å / % possible obs: 98 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.814 / Num. measured all: 38067 / Num. unique obs: 5811 / CC1/2: 0.838 / Rpim(I) all: 0.334 / Rrim(I) all: 0.885 / Χ2: 0.83 / Net I/σ(I) obs: 2.7

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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: 2.44→50.48 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2636 1850 5.04 %
Rwork0.2402 --
obs0.2414 36684 88.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→50.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6398 0 52 48 6498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036594
X-RAY DIFFRACTIONf_angle_d0.5578912
X-RAY DIFFRACTIONf_dihedral_angle_d5.696890
X-RAY DIFFRACTIONf_chiral_restr0.042949
X-RAY DIFFRACTIONf_plane_restr0.0051152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.520.37392340.3333693X-RAY DIFFRACTION97
2.52-2.620.34631920.32263868X-RAY DIFFRACTION99
2.62-2.740.28011370.3132430X-RAY DIFFRACTION62
2.74-2.890.31151930.29823857X-RAY DIFFRACTION100
2.89-3.070.3142090.29453899X-RAY DIFFRACTION100
3.07-3.30.29952050.27333908X-RAY DIFFRACTION100
3.3-3.620.28041290.24752673X-RAY DIFFRACTION71
3.7-4.160.24471260.21252395X-RAY DIFFRACTION72
4.16-5.240.1872040.17663993X-RAY DIFFRACTION100
5.25-50.480.25612210.22114118X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -23.8041 Å / Origin y: 22.0468 Å / Origin z: -24.0931 Å
111213212223313233
T0.2711 Å20.0097 Å2-0.0036 Å2-0.2914 Å20.0013 Å2--0.2759 Å2
L0.7665 °20.064 °20.1595 °2-0.7931 °2-0.1056 °2--0.6009 °2
S0.0206 Å °-0.0317 Å °0.0183 Å °-0.0539 Å °-0.0527 Å °0.0436 Å °0.013 Å °-0.0273 Å °0.0357 Å °
Refinement TLS groupSelection details: all

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