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- PDB-8wij: Crystal structure of E. coli ThrS catalytic domain mutant L489M i... -

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Basic information

Entry
Database: PDB / ID: 8wij
TitleCrystal structure of E. coli ThrS catalytic domain mutant L489M in complex with Obafluorin
ComponentsThreonine--tRNA ligase
KeywordsLIGASE / Threonine--tRNA ligase
Function / homologyChem-X5V / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 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
B: Threonine--tRNA ligase
A: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7756
Polymers95,8912
Non-polymers8834
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-19 kcal/mol
Surface area32750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.246, 84.244, 102.587
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: 47945.555 Da / Num. of mol.: 2 / Mutation: L489M
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-X5V / N-(2,3-dihydroxybenzoyl)-4-(4-nitrophenyl)-L-threonine


Type: L-peptide NH3 amino terminus / Mass: 376.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16N2O8 / Feature type: SUBJECT OF INVESTIGATION
#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.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: .0 M ammonium sulfate, and 0.15 M sodium citrate pH 5.5. 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, 0.061 M ...Details: .0 M ammonium sulfate, and 0.15 M sodium citrate pH 5.5. 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, 0.061 M tris, 0.039 M bicine pH 8.5, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / 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: 3.08→84.24 Å / Num. obs: 15723 / % possible obs: 91.5 % / Redundancy: 6.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.082 / Rrim(I) all: 0.208 / Χ2: 0.99 / Net I/σ(I): 9.4 / Num. measured all: 100869
Reflection shellResolution: 3.08→3.25 Å / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 1.051 / Num. measured all: 16724 / Num. unique obs: 2479 / CC1/2: 0.716 / Rpim(I) all: 0.435 / Rrim(I) all: 1.139 / Χ2: 0.95 / Net I/σ(I) obs: 2.6

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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: 3.08→36.39 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2784 764 4.88 %
Rwork0.2379 --
obs0.24 15641 91.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.08→36.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6487 0 54 12 6553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026683
X-RAY DIFFRACTIONf_angle_d0.4679009
X-RAY DIFFRACTIONf_dihedral_angle_d5.003918
X-RAY DIFFRACTIONf_chiral_restr0.041938
X-RAY DIFFRACTIONf_plane_restr0.0041178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.320.34161930.32983182X-RAY DIFFRACTION100
3.32-3.630.3316920.29852243X-RAY DIFFRACTION73
3.69-4.180.29571410.27612837X-RAY DIFFRACTION97
4.18-5.260.26771830.21583235X-RAY DIFFRACTION100
5.26-36.390.24121550.1893380X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 15.9899 Å / Origin y: -1.0972 Å / Origin z: -10.3288 Å
111213212223313233
T0.4774 Å2-0.0027 Å20.0556 Å2-0.381 Å20.0181 Å2--0.4642 Å2
L1.0773 °2-0.3152 °2-0.1081 °2-0.4988 °20.1196 °2--0.8893 °2
S-0.0875 Å °-0.0666 Å °-0.1577 Å °0.0641 Å °-0.0197 Å °0.0128 Å °0.1845 Å °0.0234 Å °0.1042 Å °
Refinement TLS groupSelection details: all

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