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

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Basic information

Entry
Database: PDB / ID: 5xii
TitleCrystal Structure of Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in complex with inhibitor 6
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 editing activity / ATP binding / cytoplasm
Similarity search - Function
C-terminal domain of ProRS / 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 ...C-terminal domain of ProRS / 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 / 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-86X / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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.pdbx_ptnr2_label_alt_id / _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)236,25038
Polymers231,7494
Non-polymers4,50134
Water12,899716
1
A: Prolyl-tRNA synthetase (ProRS)
C: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,06817
Polymers115,8752
Non-polymers2,19315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-54 kcal/mol
Surface area37840 Å2
MethodPISA
2
B: Prolyl-tRNA synthetase (ProRS)
D: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,18321
Polymers115,8752
Non-polymers2,30819
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9250 Å2
ΔGint-97 kcal/mol
Surface area37240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.600, 90.730, 92.996
Angle α, β, γ (deg.)89.940, 99.370, 104.310
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 / Mutation: 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 , 6 types, 750 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-86X / 6-chloranyl-7-fluoranyl-3-[3-[(2R)-3-oxidanylidenepiperidin-2-yl]propyl]quinazolin-4-one


Mass: 337.776 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H17ClFN3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 716 / 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: 53.83 %
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: 0.9797 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 123090 / % possible obs: 98.1 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.031 / Rrim(I) all: 0.052 / Χ2: 0.82 / Net I/σ(I): 11 / Num. measured all: 337845
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.17-2.212.60.479587858780.7030.3760.6120.92793.5
2.21-2.252.70.42461210.7960.3270.5380.93497.5
2.25-2.292.70.3760780.830.2820.4670.91597.4
2.29-2.342.70.33961230.8470.2560.4270.91797.6
2.34-2.392.80.361620.8840.2240.3760.94497.7
2.39-2.442.80.26661680.9030.1990.3340.91397.8
2.44-2.512.80.21960900.9250.1640.2750.91697.7
2.51-2.572.80.17661360.9470.1310.2210.88598.1
2.57-2.652.80.14761710.9640.1110.1850.86898
2.65-2.732.80.12561380.9710.0940.1580.89898.3
2.73-2.832.80.09862180.9820.0740.1240.85298.3
2.83-2.952.80.07861450.9860.0590.0990.8598.4
2.95-3.082.80.05961980.990.0450.0740.82198.6
3.08-3.242.80.04361500.9940.0330.0550.79398.6
3.24-3.442.80.03362120.9950.0250.0420.78998.9
3.44-3.712.80.02661740.9960.020.0330.76998.9
3.71-4.082.80.02262180.9960.0170.0280.81599.1
4.08-4.672.80.01762320.9970.0130.0210.65899.3
4.67-5.892.80.01562640.9980.0110.0190.5399.5
5.89-502.70.01162140.9990.0080.0130.43899.3

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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: 2.17→40.29 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2121 / WRfactor Rwork: 0.1636 / FOM work R set: 0.8479 / SU B: 5.184 / SU ML: 0.131 / SU R Cruickshank DPI: 0.2272 / SU Rfree: 0.1899 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 6101 5 %RANDOM
Rwork0.1748 ---
obs0.1773 115317 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.82 Å2 / Biso mean: 33.867 Å2 / Biso min: 7.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.01 Å2-0.07 Å2
2--0.14 Å20.01 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 2.17→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15288 0 367 730 16385
Biso mean--29.63 34.82 -
Num. residues----1900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01916260
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.97122074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37851929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12723.176721
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.546152720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6215115
X-RAY DIFFRACTIONr_chiral_restr0.1050.22315
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112282
LS refinement shellResolution: 2.175→2.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 378 -
Rwork0.262 6656 -
all-7034 -
obs--75.85 %

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