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- PDB-5xiq: Crystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (Tg... -

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Basic information

Entry
Database: PDB / ID: 5xiq
TitleCrystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with Halofuginone
ComponentsProlyl-tRNA synthetase (ProRS)
KeywordsLIGASE / Protein Translation / PRS / Synthetase / Inhibitor / Infectious Disease
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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-HFG / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsJain, V. / Manickam, Y. / Sharma, A.
CitationJournal: Structure / Year: 2017
Title: Targeting Prolyl-tRNA Synthetase to Accelerate Drug Discovery against Malaria, Leishmaniasis, Toxoplasmosis, Cryptosporidiosis, and Coccidiosis
Authors: Jain, V. / Yogavel, M. / Kikuchi, H. / Oshima, Y. / Hariguchi, N. / Matsumoto, M. / Goel, P. / Touquet, B. / Jumani, R.S. / Tacchini-Cottier, F. / Harlos, K. / Huston, C.D. / Hakimi, M.A. / Sharma, A.
History
DepositionApr 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prolyl-tRNA synthetase (ProRS)
B: Prolyl-tRNA synthetase (ProRS)
C: Prolyl-tRNA synthetase (ProRS)
D: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,62720
Polymers231,7494
Non-polymers3,87816
Water6,990388
1
A: Prolyl-tRNA synthetase (ProRS)
B: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,81310
Polymers115,8752
Non-polymers1,9398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-52 kcal/mol
Surface area38350 Å2
MethodPISA
2
C: Prolyl-tRNA synthetase (ProRS)
D: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,81310
Polymers115,8752
Non-polymers1,9398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-56 kcal/mol
Surface area38430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.852, 90.898, 92.869
Angle α, β, γ (deg.)89.860, 80.920, 75.820
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Prolyl-tRNA synthetase (ProRS)


Mass: 57937.258 Da / Num. of mol.: 4 / Fragment: UNP residues 334-830
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (strain ATCC 50611 / Me49) (eukaryote)
Strain: ATCC 50611 / Me49 / Gene: TGME49_219850 / Plasmid: PETM41 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: S8G8I1, proline-tRNA ligase
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-HFG / 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one / Halofuginone


Mass: 414.681 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H17BrClN3O3 / Comment: alkaloid, medication*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10%(w/v) PEG 4K, 20%(v/v) glycerol, 0.03M of each divalent cation and 0.1M MES/imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95373 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 120215 / % possible obs: 98.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.091 / Χ2: 1.4 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.2-2.243.70.57158690.721197.5
2.24-2.283.80.4870.731197.7

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Processing

Software
NameVersionClassification
MxCuBEdata reduction
HKL-2000data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TWA

4twa


Resolution: 2.19→40.32 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.891 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.176
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 6057 5 %RANDOM
Rwork0.1654 ---
obs0.1676 114158 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 142.14 Å2 / Biso mean: 44.414 Å2 / Biso min: 13.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.45 Å20.73 Å2
2--1.21 Å2-0.43 Å2
3----0.82 Å2
Refinement stepCycle: final / Resolution: 2.19→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15579 0 240 392 16211
Biso mean--34.8 40.5 -
Num. residues----1918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01916432
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215456
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.96522303
X-RAY DIFFRACTIONr_angle_other_deg0.9573.00235693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79151944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32323.236754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.396152875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.09415123
X-RAY DIFFRACTIONr_chiral_restr0.1120.22340
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02118059
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023810
LS refinement shellResolution: 2.192→2.249 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 358 -
Rwork0.228 7467 -
all-7825 -
obs--85.55 %

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