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- PDB-6a88: Crystal Structure of T. gondii prolyl tRNA synthetase with Febrif... -

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Basic information

Entry
Database: PDB / ID: 6a88
TitleCrystal Structure of T. gondii prolyl tRNA synthetase with Febrifugine and ATP Analog
ComponentsProlyl-tRNA synthetase (ProRS)
KeywordsTRANSLATION / PRS / Drug / Parasite / ATP
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-9SF / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / proline--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.596 Å
AuthorsKumari, S. / Mishra, S. / Yogavel, M. / Sharma, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Conformational heterogeneity in apo and drug-bound structures of Toxoplasma gondii prolyl-tRNA synthetase.
Authors: Mishra, S. / Malhotra, N. / Kumari, S. / Sato, M. / Kikuchi, H. / Yogavel, M. / Sharma, A.
History
DepositionJul 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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)235,07616
Polymers231,7494
Non-polymers3,32712
Water4,612256
1
A: Prolyl-tRNA synthetase (ProRS)
B: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,5388
Polymers115,8752
Non-polymers1,6646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-41 kcal/mol
Surface area38670 Å2
MethodPISA
2
C: Prolyl-tRNA synthetase (ProRS)
D: Prolyl-tRNA synthetase (ProRS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,5388
Polymers115,8752
Non-polymers1,6646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-40 kcal/mol
Surface area38440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.910, 90.882, 93.028
Angle α, β, γ (deg.)89.910, 80.300, 75.580
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 ME49 (eukaryote) / Strain: Me49 / Gene: TGME49_219850 / Production host: Escherichia coli (E. coli) / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-9SF / 3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one


Mass: 301.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H19N3O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: Published

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.59→42.83 Å / Num. obs: 73015 / % possible obs: 98.8 % / Redundancy: 3.4 % / CC1/2: 0.987 / Χ2: 0.89 / Net I/σ(I): 7.6
Reflection shellResolution: 2.59→2.67 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5337 / CC1/2: 0.675 / Χ2: 0.82 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.79 Å42.77 Å
Translation2.79 Å42.77 Å

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Processing

Software
NameVersionClassification
PHENIX1.15rc2_3428refinement
PHASER2.8.0phasing
PDB_EXTRACT3.24data extraction
DIALSdata reduction
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5xif

5xif


Resolution: 2.596→39.94 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 3659 5.02 %
Rwork0.1723 69251 -
obs0.1746 72910 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.99 Å2 / Biso mean: 46.1647 Å2 / Biso min: 12.02 Å2
Refinement stepCycle: final / Resolution: 2.596→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15679 0 216 256 16151
Biso mean--34.39 40.7 -
Num. residues----1915
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5964-2.63050.27561340.22992320245487
2.6305-2.66660.31361460.23062682282898
2.6666-2.70470.27921410.23032606274798
2.7047-2.7450.31841460.22042687283398
2.745-2.78790.26151590.22082627278698
2.7879-2.83360.29291370.20072722285998
2.8336-2.88250.29211250.20262646277198
2.8825-2.93490.25171480.20252647279598
2.9349-2.99130.27011600.2032626278698
2.9913-3.05230.23331370.19532684282199
3.0523-3.11870.26721530.19292658281199
3.1187-3.19120.26451420.19392713285599
3.1912-3.27090.24441780.17442614279299
3.2709-3.35930.2272930.18012739283299
3.3593-3.45810.21721500.18042670282099
3.4581-3.56970.23351160.18072696281299
3.5697-3.69720.22241180.17712738285699
3.6972-3.84510.24311420.16592684282699
3.8451-4.020.21091520.16452639279199
4.02-4.23170.18281460.1532699284599
4.2317-4.49650.19721340.13662713284799
4.4965-4.84310.14041540.1312679283399
4.8431-5.32950.16831530.1412664281799
5.3295-6.09830.22161000.16852746284699
6.0983-7.67430.18961460.172527002846100
7.6743-39.94430.20441490.16062652280198

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