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

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Basic information

Entry
Database: PDB / ID: 7fal
TitleCo-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with T36 and L-pro
ComponentsProlyl-tRNA synthetase (ProRS)
KeywordsTRANSLATION/INHIBITOR / Inhibitor-Bound Structural Comparison / TRANSLATION / 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 / ATP 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-1T0 / PROLINE / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.219 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 1.0Aug 31, 2022Provider: 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

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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)117,0786
Polymers115,8752
Non-polymers1,2034
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-23 kcal/mol
Surface area39100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.011, 86.333, 104.462
Angle α, β, γ (deg.)90.000, 102.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-1T0 / 4-[(3R)-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.: 2 / Source method: isolated from a natural source / Formula: C27H27FN6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
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: 3.01 Å3/Da / Density % sol: 59.12 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Morpheus E2

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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: 3.219→67.3 Å / Num. obs: 22703 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 1 / Net I/σ(I): 4.6
Reflection shellResolution: 3.27→3.33 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1124 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX1.15rc2_3428refinement
PDB_EXTRACT3.25data extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6aa0

6aa0


Resolution: 3.219→54.741 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 1009 4.7 %
Rwork0.2289 20476 -
obs0.2301 21485 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.5 Å2 / Biso mean: 52.662 Å2 / Biso min: 6.57 Å2
Refinement stepCycle: final / Resolution: 3.219→54.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7816 0 88 7 7911
Biso mean--54.8 21.05 -
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 (%)
3.219-3.38840.33671430.3233287798
3.3884-3.60070.31011460.27232939100
3.6007-3.87860.29821270.26452899100
3.8786-4.26880.25971590.23262909100
4.2688-4.88620.20611360.18882925100
4.8862-6.15470.22721740.204291999
6.1547-54.740.21111240.1939300899
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)
11.89220.0997-0.21381.8439-0.48371.97280.09120.3587-0.2159-0.07210.0085-0.11780.6136-0.0602-0.07360.36230.0198-0.05560.33690.01120.36897.7016-9.902422.5659
22.07530.2168-0.10481.3122-0.13021.3030.2028-0.0415-0.41120.0196-0.252-0.30030.29510.1810.03250.32180.1160.02110.2940.07010.331822.0026-9.455628.7762
31.9652-1.1157-0.31191.6698-0.35231.62450.07960.13430.6037-0.18650.20560.1271-0.3516-0.5249-0.18960.19820.0410.08940.45720.11380.5245-12.08396.869731.2298
42.0852-0.5737-0.76383.5109-0.08773.32960.1614-0.3009-0.33090.1291-0.061-0.16370.5761-0.0749-0.17050.3529-0.0593-0.02830.28880.11920.354312.8572-24.66448.8271
57.9045-2.6722.96822-5.67483.5131-0.1647-0.0146-0.5162-0.7819-0.1655-0.6210.63660.40690.33360.54140.2896-0.0180.6956-0.33450.782221.0273-12.198227.8739
62.04520.4529-0.03081.8413-0.75482.0110.10140.2331-0.251-0.2781-0.1523-0.01830.42850.03920.05790.3840.0962-0.00040.3349-0.04970.322320.4722-1.79887.9885
70.7636-0.14370.32380.6989-0.30581.81390.04090.1491-0.0094-0.1494-0.05680.02950.1150.05620.05890.29240.0621-0.00540.23910.00680.276516.00089.05870.8642
87.41016.8336-3.24336.7096-1.34348.0789-0.18370.6198-0.1189-1.2540.56440.42192.4052-0.4337-0.38480.81720.2899-0.3940.665-0.05530.97128.336-3.1277-0.1737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 331 through 423 )A331 - 423
2X-RAY DIFFRACTION2chain 'A' and (resid 424 through 603 )A424 - 603
3X-RAY DIFFRACTION3chain 'A' and (resid 604 through 734 )A604 - 734
4X-RAY DIFFRACTION4chain 'A' and (resid 735 through 830 )A735 - 830
5X-RAY DIFFRACTION5chain 'A' and (resid 902 through 902 )A902
6X-RAY DIFFRACTION6chain 'B' and (resid 331 through 428 )B331 - 428
7X-RAY DIFFRACTION7chain 'B' and (resid 429 through 830 )B429 - 830
8X-RAY DIFFRACTION8chain 'B' and (resid 902 through 902 )B902

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