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- PDB-7vc5: Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 7vc5
TitleToxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor T35 and Febrifugine (FF) at 1.61 A resolution
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 synthetase multienzyme complex / aminoacyl-tRNA deacylase activity / ATP binding / metal ion 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
Chem-1TI / Chem-9SF / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.612 Å
AuthorsManickam, Y. / Malhotra, N. / Sharma, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR32713 India
CitationJournal: To Be Published
Title: TgPRS with double inhibitors
Authors: Malhotra, N. / Manickam, Y. / Sharma, A.
History
DepositionSep 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,42613
Polymers57,9371
Non-polymers1,48912
Water5,513306
1
A: Prolyl-tRNA synthetase (ProRS)
hetero molecules

A: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,85226
Polymers115,8752
Non-polymers2,97724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7370 Å2
ΔGint-29 kcal/mol
Surface area38680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.194, 73.092, 74.936
Angle α, β, γ (deg.)90.000, 111.570, 90.000
Int Tables number5
Space group name H-MC121

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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 , 6 types, 318 molecules

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


Mass: 486.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27FN6O2 / 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.: 1 / Source method: obtained synthetically / Formula: C16H19N3O3 / Comment: alkaloid*YM
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 51.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Amino acids (0.2M DL-Glutamic acid monohydrate, 0.2M DL-Alanine, 0.2M Glycine, 0.2M DL-Lysine monohydrochloride and 0.2M DL-Serine), 0.1 M Buffer (Imidazole; MES monohydrate), 30 % v/v ...Details: 0.1 M Amino acids (0.2M DL-Glutamic acid monohydrate, 0.2M DL-Alanine, 0.2M Glycine, 0.2M DL-Lysine monohydrochloride and 0.2M DL-Serine), 0.1 M Buffer (Imidazole; MES monohydrate), 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: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.61→60.38 Å / Num. obs: 74455 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 1 / Rrim(I) all: 0.05 / Net I/σ(I): 15.4
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 6.6 % / Num. unique obs: 3674 / CC1/2: 0.3 / Rrim(I) all: 2.511 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F9S

7f9s


Resolution: 1.612→53.562 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1956 3638 4.9 %
Rwork0.165 70604 -
obs0.1665 74242 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.66 Å2 / Biso mean: 43.699 Å2 / Biso min: 22.72 Å2
Refinement stepCycle: final / Resolution: 1.612→53.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 100 310 4298
Biso mean--44.85 53.95 -
Num. residues----485
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6123-1.63350.34461230.3439257295
1.6335-1.65590.32271550.311267999
1.6559-1.67960.33181560.31652658100
1.6796-1.70460.29771280.28362770100
1.7046-1.73130.31281310.26792662100
1.7313-1.75970.26841590.24172711100
1.7597-1.790.25621430.23242724100
1.79-1.82260.27791490.21982695100
1.8226-1.85760.23561350.20352715100
1.8576-1.89550.21961670.20182699100
1.8955-1.93680.24771410.19882724100
1.9368-1.98180.26071480.17942680100
1.9818-2.03140.21051390.1732739100
2.0314-2.08630.19891150.17552738100
2.0863-2.14770.20141150.16982744100
2.1477-2.2170.18631360.16372753100
2.217-2.29630.19781510.17232666100
2.2963-2.38820.21491360.17092733100
2.3882-2.49690.18551340.17912730100
2.4969-2.62850.19811330.17552744100
2.6285-2.79320.20281560.17932678100
2.7932-3.00890.21261320.17252763100
3.0089-3.31160.19531390.16792720100
3.3116-3.79070.18941340.15062771100
3.7907-4.77540.15331470.1292735100
4.7754-53.5620.18221360.1475280199
Refinement TLS params.Method: refined / Origin x: 15.1759 Å / Origin y: -0.1602 Å / Origin z: 8.2585 Å
111213212223313233
T0.2725 Å20.0113 Å2-0.0135 Å2-0.2631 Å20.0424 Å2--0.2855 Å2
L1.1777 °2-0.3264 °2-0.1985 °2-0.831 °20.1419 °2--0.8234 °2
S-0.006 Å °0.0208 Å °0.0175 Å °0.0498 Å °-0.004 Å °-0.1501 Å °0.1024 Å °0.0592 Å °0.0075 Å °
Refinement TLS groupSelection details: all

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