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

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Basic information

Entry
Database: PDB / ID: 8wii
TitleCrystal structure of E. coli ThrS catalytic domain mutant G463A in complex with Obafluorin
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: 2.98 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)96,7316
Polymers95,8832
Non-polymers8474
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-19 kcal/mol
Surface area33590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.402, 108.812, 113.771
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
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-WE3 / ~{N}-[(2~{R},3~{S})-2-[(4-nitrophenyl)methyl]-4-oxidanylidene-oxetan-3-yl]-2,3-bis(oxidanyl)benzamide / Obafluorin


Mass: 358.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14N2O7 / 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
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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D-glucosamine, 0.05 M sodium HEPES, 0.05 M MOPS acid pH 7.5, 12.5% v/v MPD, 12.5% ...Details: 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D-glucosamine, 0.05 M sodium HEPES, 0.05 M MOPS acid pH 7.5, 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: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.98→78.64 Å / Num. obs: 23547 / % possible obs: 99.6 % / Redundancy: 4.2 % / CC1/2: 0.995 / Net I/σ(I): 6.8
Reflection shellResolution: 2.98→3.14 Å / Num. unique obs: 3379 / CC1/2: 0.773

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→78.64 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.298 1113 4.74 %
Rwork0.2457 --
obs0.2481 23478 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.98→78.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6545 0 54 0 6599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076743
X-RAY DIFFRACTIONf_angle_d1.2429087
X-RAY DIFFRACTIONf_dihedral_angle_d11.64898
X-RAY DIFFRACTIONf_chiral_restr0.061942
X-RAY DIFFRACTIONf_plane_restr0.0161190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.110.33891280.35272758X-RAY DIFFRACTION100
3.11-3.280.38391540.32272748X-RAY DIFFRACTION100
3.28-3.480.34951470.30232752X-RAY DIFFRACTION100
3.48-3.750.31181490.27772767X-RAY DIFFRACTION100
3.75-4.130.30791190.26082809X-RAY DIFFRACTION100
4.13-4.720.29081270.21292808X-RAY DIFFRACTION100
4.72-5.950.27251430.22122813X-RAY DIFFRACTION99
5.95-78.640.25061460.19162910X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -24.571 Å / Origin y: 21.9069 Å / Origin z: -24.0736 Å
111213212223313233
T0.2896 Å20.0264 Å2-0.0214 Å2-0.3916 Å20.0019 Å2--0.329 Å2
L0.673 °2-0.0538 °20.0344 °2-1.5636 °2-0.1839 °2--0.6414 °2
S-0.0587 Å °0.0388 Å °-0.0015 Å °0.2138 Å °0.0326 Å °0.0865 Å °-0.0424 Å °-0.0282 Å °0.0354 Å °
Refinement TLS groupSelection details: all

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