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

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Basic information

Entry
Database: PDB / ID: 5xik
TitleCrystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with tetrahydro quinazolinone febrifugine
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-87C / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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)235,33224
Polymers231,7494
Non-polymers3,58320
Water3,711206
1
A: Prolyl-tRNA synthetase (ProRS)
B: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,63011
Polymers115,8752
Non-polymers1,7569
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-61 kcal/mol
Surface area37720 Å2
MethodPISA
2
C: Prolyl-tRNA synthetase (ProRS)
D: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,70113
Polymers115,8752
Non-polymers1,82711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-78 kcal/mol
Surface area37360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.644, 90.140, 93.201
Angle α, β, γ (deg.)89.460, 80.340, 76.070
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 226 molecules

#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-87C / 3-[2-oxidanylidene-3-[(2R,3R)-3-oxidanylpiperidin-2-yl]propyl]-5,6,7,8-tetrahydroquinazolin-4-one


Mass: 305.372 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H23N3O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10%(w/v) PEG 8K, 20%(v/v) ethylene glycol, 0.03M of each divalent cation and 0.1M MOPS/HEPES-Na

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.96725 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: 0.96725 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 80691 / % possible obs: 98.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.051 / Rrim(I) all: 0.093 / Χ2: 0.837 / Net I/σ(I): 7.6 / Num. measured all: 266115
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.20.5395839580.7640.3340.6040.83997.9
2.54-2.593.30.48439990.7860.3170.580.86598
2.59-2.643.30.43240560.8090.2820.5180.88598
2.64-2.693.30.39439690.8640.2560.4710.88498.2
2.69-2.753.30.33940220.8940.2190.4050.89298.2
2.75-2.823.30.29140530.9020.1890.3490.90598.3
2.82-2.893.30.24640120.9280.1590.2940.89898.4
2.89-2.963.30.21440230.9380.1390.2560.89598.4
2.96-3.053.30.17440450.9540.1130.2080.91498.5
3.05-3.153.30.14939890.9660.0970.1790.90198.6
3.15-3.263.30.11540460.9770.0750.1380.89598.7
3.26-3.393.30.08940190.9820.0590.1070.84898.8
3.39-3.553.30.07340910.9860.0480.0880.84598.8
3.55-3.733.30.06140410.9880.0410.0740.81998.9
3.73-3.973.30.05140410.9910.0350.0620.899
3.97-4.273.30.04440760.9910.030.0530.75899.2
4.27-4.73.30.04140570.9920.0280.0490.85699.3
4.7-5.383.30.03840660.9920.0260.0470.74599.5
5.38-6.783.30.0440740.9920.0270.0490.69999.6
6.78-503.20.02940540.9960.0190.0350.60399.1

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Phasing

PhasingMethod: molecular replacement

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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→43.76 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2286 / WRfactor Rwork: 0.1741 / FOM work R set: 0.8383 / SU B: 8.678 / SU ML: 0.195 / SU R Cruickshank DPI: 0.5546 / SU Rfree: 0.2889 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.555 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3988 5 %RANDOM
Rwork0.1846 ---
obs0.1876 75422 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.46 Å2 / Biso mean: 37.618 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20.15 Å2-0.1 Å2
2--0.04 Å2-0.15 Å2
3---0.7 Å2
Refinement stepCycle: final / Resolution: 2.5→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15280 0 224 214 15718
Biso mean--27.16 29.94 -
Num. residues----1888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01916134
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215216
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.96721868
X-RAY DIFFRACTIONr_angle_other_deg0.844335149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10151890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1823.311731
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.857152836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.77115117
X-RAY DIFFRACTIONr_chiral_restr0.0960.22301
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02117656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023691
LS refinement shellResolution: 2.504→2.569 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 238 -
Rwork0.259 4466 -
all-4704 -
obs--77.43 %

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