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- PDB-6aa0: Crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (Tg... -

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Basic information

Entry
Database: PDB / ID: 6aa0
TitleCrystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in Apo Form
ComponentsProlyl-tRNA synthetase (ProRS)
KeywordsTRANSLATION / Toxoplasma gondii / Proly tRNA Synthetase / Apo-Form / Inhibitor-Bound Structural Comparison.
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 / cytoplasm
Similarity search - Function
C-terminal domain of ProRS / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / Proline-tRNA ligase, class IIa / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / 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 / Proline-tRNA ligase, class IIa / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / 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
proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMishra, S. / Kumari, S. / Sharma, A. / Yogavel, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Conformational heterogeneity in apo and drug-bound structures of Toxoplasma gondii prolyl-tRNA synthetase.
Authors: Mishra, S. / Malhotra, N. / Kumari, S. / Sato, M. / Kikuchi, H. / Yogavel, M. / Sharma, A.
History
DepositionJul 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)
C: Prolyl-tRNA synthetase (ProRS)
D: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,85416
Polymers231,7494
Non-polymers1,10512
Water00
1
A: Prolyl-tRNA synthetase (ProRS)
B: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4278
Polymers115,8752
Non-polymers5536
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-14 kcal/mol
Surface area40020 Å2
MethodPISA
2
C: Prolyl-tRNA synthetase (ProRS)
D: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4278
Polymers115,8752
Non-polymers5536
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-13 kcal/mol
Surface area40960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.070, 113.070, 199.813
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Prolyl-tRNA synthetase (ProRS)


Mass: 57937.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii ME49 (eukaryote) / Strain: Me49 / Gene: TGME49_219850 / Production host: Escherichia coli (E. coli) / References: UniProt: S8G8I1, proline-tRNA ligase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
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: 3.18 Å3/Da / Density % sol: 61.35 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: Published

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980066 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980066 Å / Relative weight: 1
ReflectionResolution: 3.2→97.91 Å / Num. obs: 47193 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 74.67 Å2 / CC1/2: 0.996 / Χ2: 0.99 / Net I/σ(I): 10.3
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3515 / CC1/2: 0.844 / Χ2: 1.02 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15rc2_3428refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
DIALSdata scaling
PHASER2.8.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5xif

5xif


Resolution: 3.2→69.932 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 22.62
RfactorNum. reflection% reflection
Rfree0.2242 2267 4.81 %
Rwork0.1883 --
obs0.1899 47105 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 199.11 Å2 / Biso mean: 76.9758 Å2 / Biso min: 29.62 Å2
Refinement stepCycle: final / Resolution: 3.2→69.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15065 0 72 0 15137
Biso mean--82.49 --
Num. residues----1850
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.26950.32641520.271128092961100
3.2695-3.34560.28251700.247927592929100
3.3456-3.42930.27981740.236228443018100
3.4293-3.5220.25151600.221927312891100
3.522-3.62560.2591440.220627822926100
3.6256-3.74260.2585940.208428702964100
3.7426-3.87640.25951220.202227942916100
3.8764-4.03160.23691700.206928172987100
4.0316-4.2150.23421080.198728072915100
4.215-4.43720.18911760.171927822958100
4.4372-4.71520.19841380.15228132951100
4.7152-5.07910.19271620.163327742936100
5.0791-5.59010.22471620.176428012963100
5.5901-6.39850.21871200.192828052925100
6.3985-8.05950.22191040.182328562960100
8.0595-69.94890.17181110.15992794290599

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