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- PDB-7rot: Plasmodium falciparum tyrosyl-tRNA synthetase, S234C mutant, in c... -

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Basic information

Entry
Database: PDB / ID: 7rot
TitlePlasmodium falciparum tyrosyl-tRNA synthetase, S234C mutant, in complex with ML901-Tyr
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / enzyme / tyrosyl-tRNA synthetase / malaria / inhibitor / tyrosine-AMP
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / host cell cytosol / host cell surface receptor binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, archaeal/eukaryotic-type / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Chem-66I / tyrosine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMetcalfe, R.D. / Xie, S.C. / Morton, C.J. / Tilley, L. / Griffin, M.D.W.
Funding support Japan, Australia, 2items
OrganizationGrant numberCountry
Global Health Innovative Technology FundGHIT-RFP-HTLP-H2019-104 Japan
National Health and Medical Research Council (NHMRC, Australia)APP1171794 Australia
CitationJournal: Science / Year: 2022
Title: Reaction hijacking of tyrosine tRNA synthetase as a new whole-of-life-cycle antimalarial strategy.
Authors: Xie, S.C. / Metcalfe, R.D. / Dunn, E. / Morton, C.J. / Huang, S.C. / Puhalovich, T. / Du, Y. / Wittlin, S. / Nie, S. / Luth, M.R. / Ma, L. / Kim, M.S. / Pasaje, C.F.A. / Kumpornsin, K. / ...Authors: Xie, S.C. / Metcalfe, R.D. / Dunn, E. / Morton, C.J. / Huang, S.C. / Puhalovich, T. / Du, Y. / Wittlin, S. / Nie, S. / Luth, M.R. / Ma, L. / Kim, M.S. / Pasaje, C.F.A. / Kumpornsin, K. / Giannangelo, C. / Houghton, F.J. / Churchyard, A. / Famodimu, M.T. / Barry, D.C. / Gillett, D.L. / Dey, S. / Kosasih, C.C. / Newman, W. / Niles, J.C. / Lee, M.C.S. / Baum, J. / Ottilie, S. / Winzeler, E.A. / Creek, D.J. / Williamson, N. / Parker, M.W. / Brand, S. / Langston, S.P. / Dick, L.R. / Griffin, M.D.W. / Gould, A.E. / Tilley, L.
History
DepositionAug 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: 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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine--tRNA ligase
B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1477
Polymers86,9122
Non-polymers1,2355
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-44 kcal/mol
Surface area31470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.188, 47.679, 140.630
Angle α, β, γ (deg.)90.000, 94.455, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-361-

ASN

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Components

#1: Protein Tyrosine--tRNA ligase


Mass: 43456.148 Da / Num. of mol.: 2 / Mutation: S234C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0807900 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IAR7, tyrosine-tRNA ligase
#2: Chemical ChemComp-66I / {(2R,3S,4R,5R)-5-[4-amino-3-(difluoromethoxy)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]-3,4-dihydroxyoxolan-2-yl}methyl [(2S)-2-amino-3-(4-hydroxyphenyl)propanoyl]sulfamate (non-preferred name)


Mass: 575.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23F2N7O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.25 M sodium malonate, pH 6.5, 2 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→47.33 Å / Num. obs: 46975 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 48.08 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.061 / Rrim(I) all: 0.115 / Rsym value: 0.097 / Net I/σ(I): 8.5
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4078 / CC1/2: 0.854 / Rpim(I) all: 0.621 / Rrim(I) all: 1.196 / Rsym value: 1.02

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ROR

7ror


Resolution: 2.2→46.74 Å / SU ML: 0.2723 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 28.9391
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2377 2401 5.12 %
Rwork0.2053 44478 -
obs0.207 46879 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5707 0 81 79 5867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00395900
X-RAY DIFFRACTIONf_angle_d0.57097945
X-RAY DIFFRACTIONf_chiral_restr0.0411857
X-RAY DIFFRACTIONf_plane_restr0.00381003
X-RAY DIFFRACTIONf_dihedral_angle_d14.72192253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.33081420.31452568X-RAY DIFFRACTION99.23
2.24-2.290.32461650.29822579X-RAY DIFFRACTION99.75
2.29-2.350.30481390.2832574X-RAY DIFFRACTION99.82
2.35-2.410.31351500.26782589X-RAY DIFFRACTION99.56
2.41-2.470.28341410.25552602X-RAY DIFFRACTION99.6
2.47-2.540.27571300.24682596X-RAY DIFFRACTION99.6
2.54-2.630.34851360.2582601X-RAY DIFFRACTION99.71
2.63-2.720.31021420.2552599X-RAY DIFFRACTION99.78
2.72-2.830.31441400.26462612X-RAY DIFFRACTION99.67
2.83-2.960.32231510.25652582X-RAY DIFFRACTION99.71
2.96-3.110.3291320.24642615X-RAY DIFFRACTION99.93
3.11-3.310.26611290.23812641X-RAY DIFFRACTION99.89
3.31-3.560.28361430.22292603X-RAY DIFFRACTION99.75
3.56-3.920.20421280.19112661X-RAY DIFFRACTION99.96
3.92-4.490.22111170.16572658X-RAY DIFFRACTION99.89
4.49-5.650.1871470.16812662X-RAY DIFFRACTION99.75
5.65-46.740.16791690.16122736X-RAY DIFFRACTION99.59
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5766325704-0.4947007546261.097318651080.777908294415-0.5602487147541.979930846920.0850625455867-0.0549036000496-0.1329595966240.09607402751280.10013026356-0.01822601040320.0429484805806-0.0815101939874-0.1821415629670.2769724480440.0327285314034-0.01080398534790.472867865822-0.03021193361360.33224312253914.169-2.38657.6
21.46397097913-0.2720847202420.7715685050761.811403969740.2083265908051.888758944880.0389176034179-0.0255053907184-0.247563224183-0.2166402909730.07588030808050.338874180048-0.0490588090231-0.19833833722-0.1195272879640.2999104794650.0282977644137-0.04172136770480.586864158962-0.0207372248390.426361290234-20.5222.78719.262
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 18:372 OR RESID 401:401 ) )A18 - 372
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 18:372 OR RESID 401:401 ) )A401
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 16:372 OR RESID 400:400 ) )B16 - 372
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 16:372 OR RESID 400:400 ) )B400

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