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- PDB-7v8k: Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 7v8k
TitleToxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with L-Proline
ComponentsProlyl-tRNA synthetase
KeywordsLIGASE / PROTEIN TRANSLATION / L-Proline / PRS / Toxoplasmosis
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
IMIDAZOLE / PROLINE / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 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: Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with L-Proline
Authors: Manickam, Y. / Malhotra, N. / Sharma, A.
History
DepositionAug 23, 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
B: Prolyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,15924
Polymers115,7602
Non-polymers1,39922
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-2 kcal/mol
Surface area38980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.196, 81.673, 104.660
Angle α, β, γ (deg.)90.000, 102.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Prolyl-tRNA synthetase


Mass: 57880.203 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, proline-tRNA ligase

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Non-polymers , 5 types, 210 molecules

#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
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, 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, 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: I03 / Wavelength: 0.9197 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 2.47→102 Å / Num. obs: 45661 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 1 / Rrim(I) all: 0.204 / Net I/σ(I): 8.2
Reflection shellResolution: 2.47→2.51 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2263 / CC1/2: 0.4 / Rrim(I) all: 1.429 / % possible all: 100

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Processing

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

5xif


Resolution: 2.47→68.291 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 2267 4.97 %
Rwork0.1666 43324 -
obs0.1693 45591 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.44 Å2 / Biso mean: 42.8797 Å2 / Biso min: 16.52 Å2
Refinement stepCycle: final / Resolution: 2.47→68.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7661 0 88 188 7937
Biso mean--55.15 45.85 -
Num. residues----949
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.47-2.52350.30671380.2445263299
2.5235-2.58220.29741390.23242712100
2.5822-2.64680.29081500.2279267599
2.6468-2.71840.29011310.22262685100
2.7184-2.79840.32631370.20912705100
2.7984-2.88870.25611420.20572722100
2.8887-2.99190.2621630.2012676100
2.9919-3.11170.29181310.20132710100
3.1117-3.25330.25381360.17942700100
3.2533-3.42480.24561190.16592742100
3.4248-3.63940.21811310.15682715100
3.6394-3.92040.22841610.1532691100
3.9204-4.31490.1791610.1322711100
4.3149-4.93910.15071240.12132720100
4.9391-6.22210.18561480.14962751100
6.2221-68.2910.16621560.1591277799
Refinement TLS params.Method: refined / Origin x: -14.6814 Å / Origin y: -16.6904 Å / Origin z: -33.8778 Å
111213212223313233
T0.2137 Å20.0186 Å2-0.0058 Å2-0.1886 Å20.0016 Å2--0.2535 Å2
L0.6125 °2-0.0155 °20.0336 °2-0.4351 °2-0.1176 °2--0.7996 °2
S-0.0006 Å °-0.093 Å °-0.0896 Å °-0.0047 Å °-0.0247 Å °-0.0077 Å °0.0692 Å °0.0461 Å °0.0243 Å °
Refinement TLS groupSelection details: all

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