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

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Basic information

Entry
Database: PDB / ID: 7fam
TitleCo-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with L97 and L-pro
ComponentsProlyl-tRNA synthetase (ProRS)
KeywordsTRANSLATION / Inhibitor-Bound Structural Comparison / Multi-drug
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 / metal ion binding / cytoplasm
Similarity search - Function
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 ...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 / 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-1XK / PROLINE / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsMishra, S. / Malhotra, N. / Yogavel, M. / Sharma, A.
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 1.0Sep 28, 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5303
Polymers57,9371
Non-polymers5932
Water84747
1
A: Prolyl-tRNA synthetase (ProRS)
hetero molecules

A: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0606
Polymers115,8752
Non-polymers1,1854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4660 Å2
ΔGint-28 kcal/mol
Surface area39680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.488, 74.039, 74.854
Angle α, β, γ (deg.)90.000, 111.240, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 477.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C26H28FN5O3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.58 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Morpheus H3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9804 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9804 Å / Relative weight: 1
ReflectionResolution: 2.42→52.874 Å / Num. obs: 22556 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.985 / Net I/σ(I): 7.4
Reflection shellResolution: 2.42→2.48 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1640 / CC1/2: 0.898

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Processing

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

6aa0


Resolution: 2.42→52.874 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 1076 4.78 %
Rwork0.1822 21458 -
obs0.1845 22534 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.52 Å2 / Biso mean: 57.7333 Å2 / Biso min: 28.4 Å2
Refinement stepCycle: final / Resolution: 2.42→52.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 35 47 4006
Biso mean--52.64 51.02 -
Num. residues----481
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.42-2.52990.27691220.2333262999
2.5299-2.66330.28921290.21812665100
2.6633-2.83010.2911480.21832683100
2.8301-3.04860.26181420.21742657100
3.0486-3.35540.26391300.20532677100
3.3554-3.84080.21291520.18782680100
3.8408-4.83840.1981120.15212720100
4.8384-52.8740.21891410.16452747100
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)
12.00750.1281-0.01731.25760.65192.86610.04550.109-0.2102-0.0582-0.0406-0.10540.33410.169-0.00680.41380.0669-0.01880.3270.03410.376512.9244-5.532-0.4615
21.3745-0.5782-0.55661.09660.13791.05820.1246-0.13370.15840.0417-0.0652-0.2059-0.10060.276-0.05520.5078-0.0359-0.09550.5145-0.00610.384218.23946.191318.2061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 333 through 603 )A333 - 603
2X-RAY DIFFRACTION2chain 'A' and (resid 604 through 1001 )A604 - 1001

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