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- PDB-7f9v: Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 7f9v
TitleToxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor T35 and Halofuginone
ComponentsProlyl-tRNA synthetase (ProRS)
KeywordsLIGASE/LIGASE INHIBITOR / PROTEIN TRANSLATION / INHIBITOR / PRS / ATP POCKET / DOUBLE DRUG / LIGASE / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / aminoacyl-tRNA deacylase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / Proline-tRNA ligase, class IIa / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II ...YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / Proline-tRNA ligase, class IIa / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / 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)
Similarity search - Domain/homology
Chem-1TI / BETA-MERCAPTOETHANOL / BROMIDE ION / FLUORIDE ION / Chem-HFG / IODIDE ION / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.816 Å
AuthorsManickam, Y. / Malhotra, N. / Sharma, A.
CitationJournal: To Be Published
Title: TgPRS with double inhibitors
Authors: Malhotra, N. / Manickam, Y. / Sharma, A.
History
DepositionJul 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 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: Prolyl-tRNA synthetase (ProRS)
B: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,84828
Polymers115,8752
Non-polymers3,97326
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-20 kcal/mol
Surface area37720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.067, 82.981, 105.521
Angle α, β, γ (deg.)90.000, 103.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Prolyl-tRNA synthetase (ProRS)


Mass: 57937.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGRH88_057780 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J6JUK2

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Non-polymers , 9 types, 593 molecules

#2: Chemical ChemComp-1TI / 4-[(3S)-3-cyano-3-(1-methylcyclopropyl)-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(1-methylpyrazol-4-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide


Mass: 486.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H27FN6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HFG / 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one / Halofuginone


Mass: 414.681 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17BrClN3O3 / Comment: medication*YM
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#7: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#8: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: F
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.09 M Halogens (0.3M Sodium fluoride, 0.3M Sodium bromide, 0.3M Sodium iodide), 0.1 M Buffer (Imidazole, MES monohydrate), 30 % v/v Precipitant (40% v/v Glycerol, 20% w/v PEG 4000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.816→75.07 Å / Num. obs: 116774 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 1 / Net I/σ(I): 10.6
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 6.7 % / Num. unique obs: 5874 / CC1/2: 0.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XIQ

5xiq


Resolution: 1.816→75.067 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1968 5779 4.96 %
Rwork0.1715 110663 -
obs0.1728 116442 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.52 Å2 / Biso mean: 44.7347 Å2 / Biso min: 25.36 Å2
Refinement stepCycle: final / Resolution: 1.816→75.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7734 0 161 576 8471
Biso mean--44.58 51.67 -
Num. residues----955
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.816-1.83660.37281760.3324355095
1.8366-1.85820.32951770.3147358298
1.8582-1.88090.29552070.2976365999
1.8809-1.90470.31551940.28243650100
1.9047-1.92980.33191890.27893729100
1.9298-1.95620.25791780.263667100
1.9562-1.98420.27141740.24613702100
1.9842-2.01380.26561870.23273676100
2.0138-2.04530.26422140.22173641100
2.0453-2.07880.23211780.21543734100
2.0788-2.11460.24161940.20953674100
2.1146-2.15310.23141970.19373711100
2.1531-2.19450.21251780.18953699100
2.1945-2.23930.22611880.18723676100
2.2393-2.2880.22082270.18393643100
2.288-2.34120.21162130.17773694100
2.3412-2.39980.21171890.18073705100
2.3998-2.46470.23551870.18143686100
2.4647-2.53720.212090.17413664100
2.5372-2.61910.21491900.18223694100
2.6191-2.71270.20781740.18273713100
2.7127-2.82130.19492220.17843689100
2.8213-2.94970.20661590.18043733100
2.9497-3.10530.19741890.17423718100
3.1053-3.29980.20731940.17053697100
3.2998-3.55460.19371840.15693737100
3.5546-3.91230.181680.14843728100
3.9123-4.47830.15262430.13053692100
4.4783-5.6420.15661920.13753732100
5.642-75.0670.18042080.1699378899
Refinement TLS params.Method: refined / Origin x: 14.5636 Å / Origin y: 2.4297 Å / Origin z: 33.9952 Å
111213212223313233
T0.3336 Å2-0.0431 Å20.0086 Å2-0.2938 Å2-0.0167 Å2--0.3624 Å2
L0.5379 °2-0.0479 °2-0.0491 °2-0.4169 °20.2379 °2--1.1514 °2
S-0.0467 Å °0.0589 Å °-0.0613 Å °0.0857 Å °-0.0835 Å °0.0226 Å °0.1798 Å °-0.0592 Å °-0 Å °
Refinement TLS groupSelection details: all

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