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- PDB-7f9t: Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 7f9t
TitleToxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L97 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
C-terminal domain of ProRS / 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 ...C-terminal domain of ProRS / 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 / Translation Initiation Factor IF3 / Anticodon-binding domain / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / 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) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1XK / ACETATE ION / FORMIC ACID / Chem-HFG / OXAMIC ACID / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.489 Å
AuthorsMalhotra, N. / Manickam, Y. / Sharma, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR32713 India
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 1.0Oct 5, 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

Downloads & links

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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)119,06229
Polymers115,8752
Non-polymers3,18827
Water13,926773
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint2 kcal/mol
Surface area37760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.587, 70.630, 76.485
Angle α, β, γ (deg.)101.050, 92.190, 115.840
Int Tables number1
Space group name H-MP1

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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 , 8 types, 800 molecules

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


Mass: 477.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H28FN5O3 / 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-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / 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: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Carboxylic acids (0.2M Sodium formate, 0.2M Ammonium acetate, 0.2M Sodium citrate tribasic dihydrate, 0.2M Potassium sodium tartrate tetrahydrate, 0.2M Sodium oxamate), 0.1 M Buffer ...Details: 0.1 M Carboxylic acids (0.2M Sodium formate, 0.2M Ammonium acetate, 0.2M Sodium citrate tribasic dihydrate, 0.2M Potassium sodium tartrate tetrahydrate, 0.2M Sodium oxamate), 0.1 M Buffer (Imidazole; MES monohydrate), 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
ReflectionResolution: 1.489→62.92 Å / Num. obs: 203943 / % possible obs: 96.4 % / Redundancy: 3.6 % / CC1/2: 1 / Net I/σ(I): 8.1
Reflection shellResolution: 1.49→1.51 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 9732 / CC1/2: 0.6 / % possible all: 91.6

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Processing

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

5xiq


Resolution: 1.489→45.067 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1911 10113 4.97 %
Rwork0.1727 193300 -
obs0.1737 203413 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 210.93 Å2 / Biso mean: 33.2848 Å2 / Biso min: 16.13 Å2
Refinement stepCycle: final / Resolution: 1.489→45.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7766 0 209 799 8774
Biso mean--36.74 44.64 -
Num. residues----958
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4892-1.50610.34693270.3109604490
1.5061-1.52380.323330.2967622693
1.5238-1.54240.29273500.2744626294
1.5424-1.56190.29423170.2673638494
1.5619-1.58250.27253080.262625894
1.5825-1.60420.28133290.2497637494
1.6042-1.62710.25163480.2401633395
1.6271-1.65140.23793320.2318631495
1.6514-1.67720.273450.23639695
1.6772-1.70470.24473480.2253637095
1.7047-1.73410.25413360.2176639996
1.7341-1.76560.24893140.2015648996
1.7656-1.79960.22843140.1965638096
1.7996-1.83630.21142870.1956646496
1.8363-1.87620.21953320.189647796
1.8762-1.91990.21373010.1859648596
1.9199-1.96790.21623270.1894651797
1.9679-2.02110.20983470.1889647097
2.0211-2.08060.19913160.187654097
2.0806-2.14770.19973150.1813649297
2.1477-2.22450.19693710.181650697
2.2245-2.31350.20183590.1756651898
2.3135-2.41880.21613560.1825651197
2.4188-2.54630.19583320.1773657798
2.5463-2.70590.19663590.1759651798
2.7059-2.91470.19653560.1811658998
2.9147-3.2080.19053630.1708659699
3.208-3.6720.16573580.152660399
3.672-4.62560.14353940.132660299
4.6256-45.0670.1733390.1519660799
Refinement TLS params.Method: refined / Origin x: -7.6945 Å / Origin y: -26.2804 Å / Origin z: 7.5355 Å
111213212223313233
T0.2272 Å2-0.0225 Å2-0.0047 Å2-0.1926 Å20.0032 Å2--0.1906 Å2
L0.9052 °2-0.2348 °2-0.0205 °2-0.4561 °2-0.0075 °2--0.2863 °2
S0.0284 Å °-0.0025 Å °0.0226 Å °0.0059 Å °-0.009 Å °-0.0218 Å °0.0484 Å °-0.0228 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA333 - 830
2X-RAY DIFFRACTION1ALLA1001 - 1512
3X-RAY DIFFRACTION1ALLB334 - 830
4X-RAY DIFFRACTION1ALLB1001 - 1469

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