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

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Basic information

Entry
Database: PDB / ID: 5xij
TitleCrystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with Inhibitor 9
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
Chem-873 / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / diffrn_radiation_wavelength / 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_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_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)235,18220
Polymers231,7494
Non-polymers3,43316
Water5,963331
1
A: Prolyl-tRNA synthetase (ProRS)
B: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,59110
Polymers115,8752
Non-polymers1,7168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-55 kcal/mol
Surface area38080 Å2
MethodPISA
2
C: Prolyl-tRNA synthetase (ProRS)
D: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,59110
Polymers115,8752
Non-polymers1,7168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-55 kcal/mol
Surface area37440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.848, 93.158, 91.012
Angle α, β, γ (deg.)89.810, 104.520, 99.600
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-873 / 3-[(2R)-2-oxidanyl-3-[(2R,3R)-3-oxidanylpiperidin-2-yl]propyl]quinazolin-4-one


Mass: 303.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H21N3O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 54.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10%(w/v) PEG 8K, 20%(v/v) ethylene glycol, 0.03M of each ethylene glycol and 0.1M bicine/Trizma base

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 82049 / % possible obs: 98.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.047 / Rrim(I) all: 0.094 / Χ2: 0.942 / Net I/σ(I): 8.5 / Num. measured all: 325216
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.80.696405040500.7280.4130.810.96297.8
2.54-2.593.90.62140990.7790.3630.7190.93498
2.59-2.6440.55840360.8160.3240.6450.93998
2.64-2.6940.48941010.8550.2830.5650.96198.2
2.69-2.7540.4340980.8780.2490.4970.97498.2
2.75-2.8240.35740590.9190.2070.4130.96598.2
2.82-2.8940.30740950.9310.1780.3550.97698.3
2.89-2.9640.26541350.9460.1530.3060.99198.4
2.96-3.0540.20840580.9640.1210.2410.99898.4
3.05-3.1540.16841100.9760.0970.1940.97298.6
3.15-3.2640.13241020.9860.0770.1531.0198.5
3.26-3.3940.140750.9910.0580.1160.9998.8
3.39-3.5540.07741120.9940.0450.0890.97198.8
3.55-3.7340.06640970.9950.0380.0760.98898.9
3.73-3.9740.05241620.9970.030.060.97199.1
3.97-4.2740.04241090.9980.0240.0490.98499.2
4.27-4.740.03541350.9980.020.041.05799.3
4.7-5.3840.03241230.9980.0180.0370.89899.5
5.38-6.7840.03341590.9980.0190.0380.79299.6
6.78-503.90.01641340.9990.0090.0180.51199.4

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Processing

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

4twa


Resolution: 2.5→40.36 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.478 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.527 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 4043 5 %RANDOM
Rwork0.18004 ---
obs0.18308 76783 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.42 Å2 / Biso mean: 37.173 Å2 / Biso min: 6.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20.06 Å2-0.06 Å2
2--0.58 Å2-0.07 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 2.5→40.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15372 0 220 334 15926
Biso mean--25.55 30.52 -
Num. residues----1909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01916266
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215192
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.96422068
X-RAY DIFFRACTIONr_angle_other_deg0.85335060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97651929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00823.347735
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.585152800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.12515117
X-RAY DIFFRACTIONr_chiral_restr0.0920.22328
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117903
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023752
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 246 -
Rwork0.268 4690 -
all-4936 -
obs--79.94 %

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