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

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Basic information

Entry
Database: PDB / ID: 7evv
TitleCo-crystal Structure of Toxoplasma gondii Prolyl tRNA Synthetase (TgPRS) in complex with JE6 and L-pro
ComponentsProlyl-tRNA synthetase (ProRS)
KeywordsTRANSLATION / Toxoplasma gondii / Prolyl tRNA Synthetase / Inhibitor-Bound Structural Comparison / Multi-drug
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-JE6 / PROLINE / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.704 Å
AuthorsMalhotra, N. / Mishra, S. / Manickam, Y. / Sharma, A.
CitationJournal: Plos Pathog. / Year: 2022
Title: Double drugging of prolyl-tRNA synthetase provides a new paradigm for anti-infective drug development.
Authors: Manickam, Y. / Malhotra, N. / Mishra, S. / Babbar, P. / Dusane, A. / Laleu, B. / Bellini, V. / Hakimi, M.A. / Bougdour, A. / Sharma, A.
History
DepositionMay 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6996
Polymers57,9371
Non-polymers7615
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-12 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.350, 75.200, 74.740
Angle α, β, γ (deg.)90.000, 110.740, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1035-

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 , 5 types, 268 molecules

#2: Chemical ChemComp-JE6 / ~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide


Mass: 374.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N4O2 / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: JCSG+ B5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→41.85 Å / Num. obs: 62494 / % possible obs: 99.1 % / Redundancy: 2.2 % / CC1/2: 0.992 / Rrim(I) all: 0.089 / Net I/σ(I): 13.3
Reflection shellResolution: 1.7→1.71 Å / Num. unique obs: 9672 / CC1/2: 0.868 / Rrim(I) all: 0.602

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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: 1.704→31.516 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1806 3122 5 %
Rwork0.1532 59352 -
obs0.1546 62474 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.93 Å2 / Biso mean: 32.7575 Å2 / Biso min: 12.36 Å2
Refinement stepCycle: final / Resolution: 1.704→31.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3977 0 53 266 4296
Biso mean--29.78 37.93 -
Num. residues----489
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7041-1.73070.33291190.3093228385
1.7307-1.75910.28761430.23482709100
1.7591-1.78940.21921420.1982693100
1.7894-1.8220.21441430.16962719100
1.822-1.8570.21071410.16362686100
1.857-1.89490.16971420.15722686100
1.8949-1.93610.18831430.16532722100
1.9361-1.98120.1971430.15792725100
1.9812-2.03070.2041430.15792703100
2.0307-2.08560.17991420.14952710100
2.0856-2.14690.19011420.14962700100
2.1469-2.21620.16741440.15012723100
2.2162-2.29540.22031430.14952715100
2.2954-2.38730.16481410.1552707100
2.3873-2.49590.18531440.15192732100
2.4959-2.62740.16581420.15562697100
2.6274-2.79190.19471450.16392747100
2.7919-3.00740.2111420.16782713100
3.0074-3.30970.19521430.15572706100
3.3097-3.78790.16791440.1432741100
3.7879-4.76970.13971450.12682748100
4.7697-31.5160.1711460.15332787100
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)
11.197-0.0305-0.08630.74270.03831.9032-0.0343-0.0311-0.16940.0533-0.0303-0.00220.29970.0318-0.02620.18380.01710.00210.11830.01790.21056.3621-8.03164.4932
21.2382-0.09210.2930.8146-0.01221.96940.03310.1963-0.05-0.095-0.0273-0.06720.16030.38550.01240.14960.04040.0110.1720.01430.148617.7368-3.7241-4.0821
31.9893-0.9734-0.47831.2450.41331.59470.0051-0.01410.10410.0806-0.0085-0.12290.06320.2902-0.02910.143-0.0331-0.0390.24450.01230.136518.3735.684518.522
48.2523.1714-0.76685.52074.33735.05880.11220.985-1.1459-0.38920.4094-0.3185-0.20570.8059-0.56750.1848-0.0150.01870.2116-0.00410.225528.571-15.4534.017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 331 through 451 )A331 - 451
2X-RAY DIFFRACTION2chain 'A' and (resid 452 through 603 )A452 - 603
3X-RAY DIFFRACTION3chain 'A' and (resid 604 through 830 )A604 - 830
4X-RAY DIFFRACTION4chain 'A' and (resid 1001 through 1001 )A0

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