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- PDB-7f9s: Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 7f9s
TitleToxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor T35 and Febrifugine (FF)
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 / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Proline-tRNA ligase, class IIa / 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 / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Proline-tRNA ligase, class IIa / 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-1TI / Chem-9SF / BETA-MERCAPTOETHANOL / FORMIC ACID / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.861 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 1.0Oct 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1979
Polymers57,9371
Non-polymers1,2598
Water3,765209
1
A: Prolyl-tRNA synthetase (ProRS)
hetero molecules

A: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,39318
Polymers115,8752
Non-polymers2,51916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7110 Å2
ΔGint-33 kcal/mol
Surface area38780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.510, 73.650, 75.030
Angle α, β, γ (deg.)90.000, 111.390, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1117-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Prolyl-tRNA synthetase (ProRS)


Mass: 57937.258 Da / Num. of mol.: 1
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 , 7 types, 217 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.: 1 / Source method: obtained synthetically / Formula: C27H27FN6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-9SF / 3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one


Mass: 301.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N3O3 / Comment: alkaloid*YM
#4: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#7: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2 mM Divalents (0.005M Manganese(II) chloride tetrahydrate, 0.005M Cobalt(II) chloride hexahydrate , 0.005M Nickel(II) chloride hexahydrate, 0.005M Zinc acetate dihydrate), 32.5 % v/v ...Details: 2 mM Divalents (0.005M Manganese(II) chloride tetrahydrate, 0.005M Cobalt(II) chloride hexahydrate , 0.005M Nickel(II) chloride hexahydrate, 0.005M Zinc acetate dihydrate), 32.5 % v/v Precipitant (25% w/v PEG 4000, 40% w/v 1,2,6-Hexanetriol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.86→41.87 Å / Num. obs: 49540 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 1 / Net I/σ(I): 21.8
Reflection shellResolution: 1.86→1.97 Å / Mean I/σ(I) obs: 1.68 / Num. unique obs: 7923 / CC1/2: 0.82 / % possible all: 98.9

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Processing

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

5xiq


Resolution: 1.861→33.996 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 2477 5 %
Rwork0.1723 47049 -
obs0.1741 49526 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.33 Å2 / Biso mean: 51.6367 Å2 / Biso min: 28.7 Å2
Refinement stepCycle: final / Resolution: 1.861→33.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3873 0 88 217 4178
Biso mean--50.56 57.51 -
Num. residues----484
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.861-1.89660.3581320.3124251497
1.8966-1.93530.33441370.27172605100
1.9353-1.97740.26431390.24672633100
1.9774-2.02340.26361370.23582595100
2.0234-2.0740.25341350.21372577100
2.074-2.13010.2781370.2062601100
2.1301-2.19270.26151380.19972612100
2.1927-2.26350.27371370.19972613100
2.2635-2.34440.23531380.1952620100
2.3444-2.43820.23661380.18932612100
2.4382-2.54920.21181380.18692624100
2.5492-2.68350.20651370.18662600100
2.6835-2.85150.19851380.18842632100
2.8515-3.07160.22761380.18812619100
3.0716-3.38040.23191380.17662624100
3.3804-3.8690.18811390.16112634100
3.869-4.87230.17031390.13182641100
4.8723-33.9960.19511420.16212693100
Refinement TLS params.Method: refined / Origin x: 15.4715 Å / Origin y: -0.1176 Å / Origin z: 7.9652 Å
111213212223313233
T0.3044 Å2-0.0053 Å2-0.0154 Å2-0.2842 Å20.0275 Å2--0.3062 Å2
L1.2593 °2-0.4143 °2-0.2614 °2-0.7595 °20.069 °2--0.8234 °2
S0.0233 Å °-0.003 Å °0.0137 Å °0.0155 Å °-0.0328 Å °-0.1263 Å °0.0535 Å °0.0989 Å °0.0085 Å °
Refinement TLS groupSelection details: all

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