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- PDB-7vc2: Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 7vc2
TitleToxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L96 and L-proline in space group P21
ComponentsProlyl-tRNA synthetase (ProRS)
KeywordsLIGASE/LIGASE INHIBITOR / PROTEIN TRANSLATION / INHIBITOR / PRS / ATP POCKET / LIGASE / LIGASE-LIGASE 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 / PROLINE / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.096 Å
AuthorsYogavel, M. / Malhotra, N. / Sharma, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR32713 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
DepositionSep 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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)117,88419
Polymers115,8752
Non-polymers2,01017
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-3 kcal/mol
Surface area38290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.100, 81.620, 104.880
Angle α, β, γ (deg.)90.000, 102.680, 90.000
Int Tables number4
Space group name H-MP1211

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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 , 5 types, 433 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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.12 M Ethylene glycols (0.3M Diethylene glycol, 0.3M Triethylene glycol, 0.3M Tetraethylene glycol, 0.3M Pentaethylene glycol), 0.1 M Buffer (Imidazole; MES monohydrate), 30% v/v ...Details: 0.12 M Ethylene glycols (0.3M Diethylene glycol, 0.3M Triethylene glycol, 0.3M Tetraethylene glycol, 0.3M Pentaethylene glycol), 0.1 M Buffer (Imidazole; MES monohydrate), 30% v/v Precipitant Mix (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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.096→47.42 Å / Num. obs: 145446 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC1/2: 1 / Net I/σ(I): 13.5
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 22375 / CC1/2: 0.74

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Processing

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

5xif


Resolution: 2.096→47.42 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.218 7280 5.01 %
Rwork0.1771 138166 -
obs0.1791 145446 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.16 Å2 / Biso mean: 51.4103 Å2 / Biso min: 29.29 Å2
Refinement stepCycle: final / Resolution: 2.096→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7635 0 139 418 8192
Biso mean--63.49 54.1 -
Num. residues----947
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.096-2.11950.31192030.3224384183
2.1195-2.14450.38322480.29844720100
2.1445-2.17060.32052360.28064500100
2.1706-2.19810.32262450.28584710100
2.1981-2.2270.32332410.27784604100
2.227-2.25750.30262460.27074663100
2.2575-2.28980.28712430.25314588100
2.2898-2.32390.29472410.25114636100
2.3239-2.36030.32562460.24484639100
2.3603-2.3990.26452420.24314652100
2.399-2.44030.26522440.22464626100
2.4403-2.48470.27492450.21054629100
2.4847-2.53250.24082430.20914634100
2.5325-2.58420.27162410.20034601100
2.5842-2.64040.2712430.19424636100
2.6404-2.70180.25392410.19024659100
2.7018-2.76930.25452480.18694648100
2.7693-2.84420.24152440.18984601100
2.8442-2.92790.23992500.1924650100
2.9279-3.02240.24792460.19274624100
3.0224-3.13040.23882420.17934611100
3.1304-3.25570.21272430.17734611100
3.2557-3.40380.23212490.17364712100
3.4038-3.58320.19952430.16564579100
3.5832-3.80760.18412440.15564606100
3.8076-4.10150.18522460.14384664100
4.1015-4.51390.16482450.13734639100
4.5139-5.16640.17042420.12734625100
5.1664-6.50640.19892480.16394614100
6.5064-47.420.17852420.164644100
Refinement TLS params.Method: refined / Origin x: 14.8761 Å / Origin y: 1.0008 Å / Origin z: 33.7923 Å
111213212223313233
T0.3961 Å2-0.0278 Å2-0.0011 Å2-0.3426 Å2-0.0159 Å2--0.4143 Å2
L0.6828 °20.0199 °2-0.076 °2-0.3519 °20.176 °2--1.0596 °2
S-0.0257 Å °0.0757 Å °-0.0761 Å °0.0403 Å °-0.0475 Å °0.0108 Å °0.1665 Å °-0.0699 Å °0 Å °
Refinement TLS groupSelection details: all

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