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- PDB-7f9q: Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 7f9q
TitleToxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L97 and Febrifugine
ComponentsProlyl-tRNA synthetase (ProRS)
KeywordsLIGASE/LIGASE INHIBITOR / PROTEIN TRANSLATION / INHIBITOR / PRS / ATP POCKET / DOUBLE DRUG / 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 / 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-1XK / Chem-9SF / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.796 Å
AuthorsManickam, Y. / Malhotra, N. / Sharma, A.
CitationJournal: To Be Published
Title: TgPRS with double inhibitors
Authors: Malhotra, N. / Manickam, Y. / Sharma, A.
History
DepositionJul 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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)117,4727
Polymers115,8752
Non-polymers1,5985
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-35 kcal/mol
Surface area37660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.479, 76.479, 407.543
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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-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.: 2 / Source method: obtained synthetically / Formula: C26H28FN5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-9SF / 3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one


Mass: 301.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19N3O3 / Comment: alkaloid*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 0.1 M Buffer (Sodium HEPES, MOPS) and 30 % v/v Precipitant (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: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.796→101.89 Å / Num. obs: 31373 / % possible obs: 100 % / Redundancy: 25.9 % / CC1/2: 1 / Net I/σ(I): 9.7
Reflection shellResolution: 2.8→2.84 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1522 / CC1/2: 0.8 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
xia2data scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XIQ

5xiq


Resolution: 2.796→19.939 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2739 973 3.13 %
Rwork0.1919 30153 -
obs0.1944 31126 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.74 Å2 / Biso mean: 68.5445 Å2 / Biso min: 22.23 Å2
Refinement stepCycle: final / Resolution: 2.796→19.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7423 0 115 18 7556
Biso mean--66.9 58.45 -
Num. residues----937
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7965-2.94350.38581280.29744205433399
2.9435-3.12730.30441420.259741544296100
3.1273-3.36760.351560.228642314387100
3.3676-3.70460.27571400.197642534393100
3.7046-4.23620.23911280.170443154443100
4.2362-5.32030.22591230.151743804503100
5.3203-19.9390.27281560.189746154771100
Refinement TLS params.Method: refined / Origin x: 20.1318 Å / Origin y: -20.6109 Å / Origin z: -24.9541 Å
111213212223313233
T0.4051 Å2-0.0085 Å20.0581 Å2-0.168 Å20.0091 Å2--0.2339 Å2
L0.4693 °20.0188 °20.0838 °2-0.8279 °20.1054 °2--0.371 °2
S0.0652 Å °-0.025 Å °0.0149 Å °-0.3505 Å °-0.1306 Å °-0.0059 Å °-0.0001 Å °-0.0313 Å °-0.001 Å °
Refinement TLS groupSelection details: all

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