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- PDB-7wmf: Threonyl-tRNA synthetase from Salmonella enterica in complex with... -

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Basic information

Entry
Database: PDB / ID: 7wmf
TitleThreonyl-tRNA synthetase from Salmonella enterica in complex with an inhibitor
ComponentsThreonine--tRNA ligase
KeywordsLIGASE/INHIBITOR / LIGASE-INHIBITOR COMPLEX
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 / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / TGS-like ...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 / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / TGS-like / tRNA synthetase class II core domain (G, H, P, S and T) / TGS domain profile. / TGS / 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-9I9 / Threonine--tRNA ligase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Cubana str. 76814 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCai, Z. / Chen, B. / Yu, Y. / Zhou, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177140 China
National Natural Science Foundation of China (NSFC)81773636 China
CitationJournal: J.Med.Chem. / Year: 2022
Title: Design, Synthesis, and Proof-of-Concept of Triple-Site Inhibitors against Aminoacyl-tRNA Synthetases.
Authors: Cai, Z. / Chen, B. / Yu, Y. / Guo, J. / Luo, Z. / Cheng, B. / Xu, J. / Gu, Q. / Zhou, H.
History
DepositionJan 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)97,4237
Polymers95,9292
Non-polymers1,4945
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-18 kcal/mol
Surface area32830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.792, 102.521, 103.171
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 47964.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Cubana str. 76814 (bacteria)
Gene: thrS / Production host: Escherichia coli (E. coli) / References: UniProt: V7II86, threonine-tRNA ligase
#2: Chemical ChemComp-9I9 / (2S,3R)-2-azanyl-N-[(1R)-2-[3-[6,7-bis(chloranyl)-4-oxidanylidene-quinazolin-3-yl]propanoylamino]-1-[3-[4-(trifluoromethyl)phenyl]phenyl]ethyl]-3-oxidanyl-butanamide


Mass: 650.476 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H28Cl2F3N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.28 M lithium acetate pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 53470 / % possible obs: 99.2 % / Redundancy: 6.6 % / CC1/2: 0.958 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.06 / Rrim(I) all: 0.154 / Χ2: 2.272 / Net I/σ(I): 20.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.146.90.54526200.9320.2210.5880.51598.3
2.14-2.186.90.45125990.9430.1830.4870.42598.9
2.18-2.226.90.39926270.9560.1630.4310.44598.9
2.22-2.266.80.44726340.9480.1840.4830.68599
2.26-2.316.70.32826480.9640.1360.3550.50998.9
2.31-2.376.60.26926190.9730.1120.2920.50798.9
2.37-2.426.50.24326280.9640.1020.2640.57899.1
2.42-2.4960.19226370.980.0840.2110.63798.4
2.49-2.566.50.19226440.9750.0810.2090.69198.5
2.56-2.656.90.18126510.9850.0740.1960.77999.4
2.65-2.746.80.17426550.980.0720.1881.02399.4
2.74-2.856.80.15526800.9830.0640.1681.0499.1
2.85-2.986.70.14226680.9740.0590.1541.57199.7
2.98-3.146.50.13426590.980.0570.1461.73399.4
3.14-3.336.10.12826930.9720.0560.1412.81699.3
3.33-3.5970.1326980.9830.0530.143.57999.7
3.59-3.956.80.13227110.980.0540.1425.10299.7
3.95-4.526.50.12827340.9610.0550.147.15299.9
4.52-5.76.30.12627530.9680.0540.1388.36999.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L2Q

6l2q


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.588 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.26 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 2622 4.9 %RANDOM
Rwork0.224 ---
obs0.226 50739 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.32 Å2 / Biso mean: 40.871 Å2 / Biso min: 25.47 Å2
Baniso -1Baniso -2Baniso -3
1-4.02 Å2-0 Å20 Å2
2---2.63 Å2-0 Å2
3----1.39 Å2
Refinement stepCycle: final / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6450 0 94 258 6802
Biso mean--52.96 44.53 -
Num. residues----802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136742
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176210
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.649117
X-RAY DIFFRACTIONr_angle_other_deg1.171.59414244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8745812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.66621.597407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7251560
X-RAY DIFFRACTIONr_chiral_restr0.0430.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028004
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021680
LS refinement shellResolution: 2.1→2.151 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.283 196 -
Rwork0.283 3547 -
obs--95.07 %

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