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- PDB-7wm7: Threonyl-tRNA synthetase from Salmonella enterica in complex with... -

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Basic information

Entry
Database: PDB / ID: 7wm7
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/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS ...Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / : / TGS domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / TGS-like / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Beta-grasp domain superfamily
Similarity search - Domain/homology
Chem-9I6 / Threonine--tRNA ligase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Cubana str. 76814 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCai, Z. / Chen, B. / Yu, Y. / Zhou, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
National Natural Science Foundation of China (NSFC) 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)97,3946
Polymers95,9292
Non-polymers1,4654
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-20 kcal/mol
Surface area32030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.473, 102.049, 103.010
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-9I6 / (2S,3R)-2-azanyl-N-[5-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)pentyl]-3-oxidanyl-N-[[3-(1-oxidanylidene-2,3-dihydroisoindol-5-yl)phenyl]methyl]butanamide


Mass: 666.993 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H33BrClN5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.34 Å3/Da / Density % sol: 47.58 %
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: Nov 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 35866 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.029 / Rrim(I) all: 0.055 / Net I/σ(I): 23.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.485 / Num. unique obs: 3720 / CC1/2: 0.946 / Rpim(I) all: 0.297 / Rrim(I) all: 0.57 / % possible all: 100

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Processing

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

6l2q


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.22 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 0.521 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2741 1873 5.2 %RANDOM
Rwork0.2284 ---
obs0.2308 33942 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.61 Å2 / Biso mean: 53.4 Å2 / Biso min: 32.68 Å2
Baniso -1Baniso -2Baniso -3
1-3.85 Å2-0 Å20 Å2
2---3.12 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: final / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6353 0 88 115 6556
Biso mean--67.85 48.19 -
Num. residues----801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136627
X-RAY DIFFRACTIONr_bond_other_d0.0030.0176062
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.6388972
X-RAY DIFFRACTIONr_angle_other_deg1.1051.59513876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4495806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.55421.554386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.999151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4131556
X-RAY DIFFRACTIONr_chiral_restr0.0380.2827
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021645
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 136 -
Rwork0.33 2478 -
all-2614 -
obs--99.81 %

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