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- PDB-7ror: Plasmodium falciparum tyrosyl-tRNA synthetase in complex with tyr... -

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Basic information

Entry
Database: PDB / ID: 7ror
TitlePlasmodium falciparum tyrosyl-tRNA synthetase in complex with tyrosine-AMP
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-69X / MALONATE ION / tyrosine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)88,68012
Polymers87,1432
Non-polymers1,53710
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-43 kcal/mol
Surface area31200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.612, 46.597, 141.402
Angle α, β, γ (deg.)90.000, 93.806, 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

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Protein , 1 types, 2 molecules AB

#1: Protein Tyrosine--tRNA ligase


Mass: 43571.281 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 341 molecules

#2: Chemical ChemComp-69X / 5'-O-[(S)-{[(2S)-2-amino-3-(4-hydroxyphenyl)propanoyl]oxy}(hydroxy)phosphoryl]adenosine


Mass: 510.394 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N6O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: 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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Details

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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.25 M sodium malonate, pH 6

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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: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→47.65 Å / Num. obs: 83538 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 36.75 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.036 / Rrim(I) all: 0.069 / Rsym value: 0.058 / Net I/σ(I): 13.3
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4539 / R split: 0.492 / Rpim(I) all: 0.862 / Rrim(I) all: 2.298 / Rsym value: 1.953

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VGJ

3vgj


Resolution: 1.8→47.65 Å / SU ML: 0.255 / Cross valid method: FREE R-VALUE / σ(F): 1.23 / Phase error: 26.88
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2178 4085 4.89 %
Rwork0.1776 79389 -
obs0.1795 83474 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5851 0 102 331 6284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01356108
X-RAY DIFFRACTIONf_angle_d1.25498223
X-RAY DIFFRACTIONf_chiral_restr0.0691881
X-RAY DIFFRACTIONf_plane_restr0.00971051
X-RAY DIFFRACTIONf_dihedral_angle_d21.13222349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.37161230.30132742X-RAY DIFFRACTION99.97
1.82-1.840.3341410.30432690X-RAY DIFFRACTION99.86
1.84-1.870.32831320.29812791X-RAY DIFFRACTION99.8
1.87-1.890.3281260.2872657X-RAY DIFFRACTION99.82
1.89-1.920.38281190.30562755X-RAY DIFFRACTION99.79
1.92-1.940.34211340.29222718X-RAY DIFFRACTION99.72
1.94-1.970.32241400.26492677X-RAY DIFFRACTION99.96
1.97-20.3311630.24612728X-RAY DIFFRACTION99.83
2-2.040.29631300.2322739X-RAY DIFFRACTION99.9
2.04-2.070.29111410.21542726X-RAY DIFFRACTION99.93
2.07-2.110.26781380.21482684X-RAY DIFFRACTION99.86
2.11-2.150.21971340.20472747X-RAY DIFFRACTION99.83
2.15-2.190.29641350.20142732X-RAY DIFFRACTION99.93
2.19-2.240.2391290.20192711X-RAY DIFFRACTION99.89
2.24-2.290.25071550.20512722X-RAY DIFFRACTION99.93
2.29-2.350.29591480.19992729X-RAY DIFFRACTION99.9
2.35-2.420.24061520.19622722X-RAY DIFFRACTION99.9
2.42-2.490.27441160.19942747X-RAY DIFFRACTION99.72
2.49-2.570.2941570.20662711X-RAY DIFFRACTION99.97
2.57-2.660.24841480.21312738X-RAY DIFFRACTION100
2.66-2.760.27021390.19932761X-RAY DIFFRACTION99.97
2.77-2.890.24261660.20762714X-RAY DIFFRACTION100
2.89-3.040.23931670.19662698X-RAY DIFFRACTION99.97
3.04-3.230.21441390.18562747X-RAY DIFFRACTION99.97
3.23-3.480.19581400.16732774X-RAY DIFFRACTION100
3.48-3.830.20741360.14642794X-RAY DIFFRACTION99.93
3.83-4.390.15491370.12562754X-RAY DIFFRACTION99.76
4.39-5.530.15991670.13232791X-RAY DIFFRACTION99.83
5.53-47.650.17341330.16482890X-RAY DIFFRACTION99.18
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)
11.34963374802-0.20497147121.358301152090.471885856275-0.5037434430372.239373425780.0982077461127-0.105239750712-0.1164416426220.00180689606203-0.004103173182290.0393696067140.0832243455464-0.0943841469013-0.09538252424670.2901576409780.045613840843-0.02051136588390.410961382034-0.03140660138340.33394418068914.444-2.78257.917
21.58594044508-0.2239426571141.198050470381.57194268809-0.03832134028261.892396071410.0240485513231-0.128404418767-0.132009995839-0.1086683311610.1403002994740.262951018523-0.002591187766-0.170353553711-0.1503032502210.2218890607780.016752734519-0.04184085974680.303156837669-0.004464307354190.375043855546-20.3542.9319.334
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 19:373 )A19 - 373
2X-RAY DIFFRACTION2( CHAIN B AND ( RESID 13:373 OR RESID 401:401 ) )B13 - 373
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 13:373 OR RESID 401:401 ) )B401

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