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- PDB-7fak: Co-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase ... -

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Basic information

Entry
Database: PDB / ID: 7fak
TitleCo-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with L96 and L-pro
ComponentsProlyl-tRNA synthetase (ProRS)
KeywordsTRANSLATION/INHIBITOR / Inhibitor-Bound Structural Comparison / Multi-drug / TRANSLATION-INHIBITOR COMPLEX
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / aminoacyl-tRNA synthetase multienzyme complex / 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-1UI / ACETATE ION / FORMIC ACID / PROLINE / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsMalhotra, N. / Mishra, S. / Yogavel, M. / Sharma, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: Plos Pathog. / Year: 2023
Title: Targeting prolyl-tRNA synthetase via a series of ATP-mimetics to accelerate drug discovery against toxoplasmosis.
Authors: Yogavel, M. / Bougdour, A. / Mishra, S. / Malhotra, N. / Chhibber-Goel, J. / Bellini, V. / Harlos, K. / Laleu, B. / Hakimi, M.A. / Sharma, A.
History
DepositionJul 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 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)59,35917
Polymers57,9371
Non-polymers1,42116
Water5,152286
1
A: Prolyl-tRNA synthetase (ProRS)
hetero molecules

A: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,71734
Polymers115,8752
Non-polymers2,84232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8820 Å2
ΔGint-29 kcal/mol
Surface area39290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.619, 74.230, 74.648
Angle α, β, γ (deg.)90.00, 111.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-903-

MES

21A-903-

MES

31A-1156-

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, 302 molecules

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


Mass: 499.536 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26FN5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.51 Å3/Da / Density % sol: 50.93 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Morpheus G2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.89→60.811 Å / Num. obs: 45141 / % possible obs: 98.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.2 Å2 / CC1/2: 1 / Rrim(I) all: 0.125 / Net I/σ(I): 8.7
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2157 / CC1/2: 0.5 / Rrim(I) all: 0.89 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.15refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6aa0

6aa0


Resolution: 1.899→60.811 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 24.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 2198 4.87 %
Rwork0.1812 --
obs0.1829 45101 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→60.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 97 286 4296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164123
X-RAY DIFFRACTIONf_angle_d1.3095567
X-RAY DIFFRACTIONf_dihedral_angle_d3.5643442
X-RAY DIFFRACTIONf_chiral_restr0.076583
X-RAY DIFFRACTIONf_plane_restr0.01727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8992-1.94050.37381430.32822574X-RAY DIFFRACTION95
1.9405-1.98560.32291480.29952635X-RAY DIFFRACTION98
1.9856-2.03530.2891560.26152597X-RAY DIFFRACTION98
2.0353-2.09030.24161220.22912684X-RAY DIFFRACTION98
2.0903-2.15180.27091570.21362632X-RAY DIFFRACTION98
2.1518-2.22130.23461280.19932668X-RAY DIFFRACTION98
2.2213-2.30070.21521210.19172678X-RAY DIFFRACTION98
2.3007-2.39280.25211360.18622685X-RAY DIFFRACTION99
2.3928-2.50170.24521380.18142695X-RAY DIFFRACTION99
2.5017-2.63360.22241310.18092695X-RAY DIFFRACTION99
2.6336-2.79860.24691280.19132695X-RAY DIFFRACTION99
2.7986-3.01470.22811350.18612691X-RAY DIFFRACTION99
3.0147-3.3180.22431330.1792708X-RAY DIFFRACTION99
3.318-3.79810.21951340.15652755X-RAY DIFFRACTION100
3.7981-4.78490.13581340.13682735X-RAY DIFFRACTION100
4.7849-60.80.18911540.1682776X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1440.10080.23571.02850.03361.69650.0466-0.0749-0.08380.14-0.0333-0.03910.26770.0088-0.01480.22970.0278-0.00370.18240.01660.2187.2716-5.54798.0425
21.5005-0.13050.17371.11720.26651.72290.06040.2229-0.155-0.1246-0.0504-0.07530.24270.1482-0.00880.21380.05990.01550.2022-0.00460.211115.7254-5.7089-4.716
31.5094-0.7968-0.68711.32930.36431.05080.0376-0.09640.05490.10290.0007-0.14150.00860.1183-0.06340.2141-0.0273-0.06330.238-0.0090.199518.34966.579218.3447
42.42473.15962.84344.39673.94763.54460.22520.2443-0.98-0.09870.1989-0.28830.40550.4474-0.44260.1694-0.0047-0.06040.2465-0.04640.293715.4687-7.9522-3.6118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 333 through 423 )
2X-RAY DIFFRACTION2chain 'A' and (resid 424 through 603 )
3X-RAY DIFFRACTION3chain 'A' and (resid 604 through 830 )
4X-RAY DIFFRACTION4chain 'A' and (resid 902 through 902 )

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