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- PDB-7f9u: Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 7f9u
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 / BROMIDE ION / Chem-HFG / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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)
C: Prolyl-tRNA synthetase (ProRS)
D: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,99726
Polymers231,7494
Non-polymers4,24822
Water90150
1
A: Prolyl-tRNA synthetase (ProRS)
D: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,02313
Polymers115,8752
Non-polymers2,14911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-55 kcal/mol
Surface area38270 Å2
MethodPISA
2
B: Prolyl-tRNA synthetase (ProRS)
C: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,97413
Polymers115,8752
Non-polymers2,10011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-79 kcal/mol
Surface area39630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.573, 76.573, 403.841
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Prolyl-tRNA synthetase (ProRS)


Mass: 57937.258 Da / Num. of mol.: 4
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 , 6 types, 72 molecules

#2: 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.: 4 / Source method: obtained synthetically / Formula: C16H17BrClN3O3 / Comment: alkaloid, medication*YM
#3: 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.: 4 / Source method: obtained synthetically / Formula: C27H27FN6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate ), 0.1 M Buffer (Sodium HEPES, MOPS), 30% v/v Precipitant (40% v/v Ethylene glycol, 20% w/v PEG 8000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.15
ReflectionResolution: 2.8→100.93 Å / Num. obs: 56889 / % possible obs: 100 % / Redundancy: 14.1 % / CC1/2: 1 / Net I/σ(I): 10.6
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2092 / CC1/2: 0.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
DIALSdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XIQ

5xiq


Resolution: 2.8→76.573 Å / Cross valid method: THROUGHOUT / σ(F): 3.47 / Phase error: 26.32 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2242 984 1.73 %
Rwork0.1636 55731 -
obs0.1659 56768 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 215.66 Å2 / Biso mean: 33.3552 Å2 / Biso min: 13.44 Å2
Refinement stepCycle: final / Resolution: 2.8→76.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15646 0 254 50 15950
Biso mean--32.86 24.45 -
Num. residues----1931
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8007-2.94820.36071430.23698018816198
2.9482-3.13280.27541600.20537834799498
3.1328-3.37450.26661410.18538005814698
3.3745-3.71370.19091000.16417995809599
3.7137-4.25010.18231460.14387969811598
4.2501-5.35110.18851580.12677926808498
5.3511-33.18980.22291340.16467984811898
Refinement TLS params.Method: refined / Origin x: 38.9614 Å / Origin y: -1.0273 Å / Origin z: 15.9088 Å
111213212223313233
T0.1279 Å2-0.0523 Å20.0158 Å2-0.1374 Å2-0.0461 Å2--0.2424 Å2
L0.457 °2-0.3393 °20.2629 °2-0.4899 °2-0.2532 °2--0.3038 °2
S-0.0008 Å °-0.0086 Å °0.0064 Å °0.0023 Å °-0.0146 Å °0.005 Å °-0.0278 Å °0.0044 Å °-0.0004 Å °
Refinement TLS groupSelection details: all

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