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- PDB-7f9r: Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 7f9r
TitleToxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L95, L-Proline and Febrifugine
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 editing activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
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 ...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 / 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-9SF / Chem-JE6 / PROLINE / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,23413
Polymers57,9371
Non-polymers1,29612
Water2,990166
1
A: Prolyl-tRNA synthetase (ProRS)
hetero molecules

A: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,46726
Polymers115,8752
Non-polymers2,59324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7710 Å2
ΔGint-21 kcal/mol
Surface area38240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.830, 73.830, 74.700
Angle α, β, γ (deg.)90.000, 111.490, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-905-

EDO

21A-1110-

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 , 6 types, 178 molecules

#2: Chemical ChemComp-JE6 / ~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide


Mass: 374.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N4O2
#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 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Amino acids (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine), 0.1 M Buffer (midazole; MES monohydrate) and 30 % v/v ...Details: 0.1 M Amino acids (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine), 0.1 M Buffer (midazole; MES monohydrate) and 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 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.83→51.34 Å / Num. obs: 51148 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 1 / Net I/σ(I): 13
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2547 / CC1/2: 0.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XIQ

5xiq


Resolution: 1.83→35.721 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1929 2585 5.05 %
Rwork0.1659 48557 -
obs0.1673 51142 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.69 Å2 / Biso mean: 56.1521 Å2 / Biso min: 30.36 Å2
Refinement stepCycle: final / Resolution: 1.83→35.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3887 0 70 167 4124
Biso mean--64.27 59.81 -
Num. residues----487
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.83-1.86520.3441550.34022695100
1.8652-1.90330.30941290.30652681100
1.9033-1.94470.31611390.2772711100
1.9447-1.98990.3041210.24142685100
1.9899-2.03970.28521310.22642695100
2.0397-2.09480.29761400.20562703100
2.0948-2.15650.2321600.2012666100
2.1565-2.22610.23941450.19122709100
2.2261-2.30560.22771440.19042658100
2.3056-2.39790.22161440.1922732100
2.3979-2.5070.25361440.19192669100
2.507-2.63910.22391420.19382721100
2.6391-2.80440.22151460.19242688100
2.8044-3.02090.21991450.18252702100
3.0209-3.32470.17881390.1701267199
3.3247-3.80530.17711590.1522270699
3.8053-4.79240.16361370.12782738100
4.7924-35.7210.16071650.1492272799
Refinement TLS params.Method: refined / Origin x: 15.1421 Å / Origin y: -0.1611 Å / Origin z: 8.1174 Å
111213212223313233
T0.3041 Å20.0181 Å2-0.0157 Å2-0.3162 Å20.0551 Å2--0.339 Å2
L1.2576 °2-0.38 °2-0.3514 °2-0.9798 °20.2673 °2--1.5163 °2
S0.0368 Å °0.0434 Å °0.0128 Å °0.0182 Å °-0.0396 Å °-0.167 Å °0.1846 Å °0.1561 Å °-0.0019 Å °
Refinement TLS groupSelection details: all

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