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- PDB-7ros: Plasmodium falciparum tyrosyl-tRNA synthetase in complex with ML9... -

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Basic information

Entry
Database: PDB / ID: 7ros
TitlePlasmodium falciparum tyrosyl-tRNA synthetase 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: 2.15 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)92,4998
Polymers91,2292
Non-polymers1,2716
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-52 kcal/mol
Surface area30370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.292, 46.529, 139.015
Angle α, β, γ (deg.)90.000, 93.772, 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: 45614.445 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
#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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.5 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: Nov 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.15→47.21 Å / Num. obs: 48258 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 41.83 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.076 / Rrim(I) all: 0.146 / Rsym value: 0.124 / Net I/σ(I): 8.4
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4197 / CC1/2: 0.655 / Rpim(I) all: 1.036 / Rrim(I) all: 2.003 / Rsym value: 1.711 / % possible all: 100

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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: 2.15→46.24 Å / SU ML: 0.2522 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 26.0807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2308 2335 4.84 %
Rwork0.2001 45878 -
obs0.2016 48213 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.44 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5719 0 82 126 5927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245913
X-RAY DIFFRACTIONf_angle_d0.45017961
X-RAY DIFFRACTIONf_chiral_restr0.0391858
X-RAY DIFFRACTIONf_plane_restr0.00261004
X-RAY DIFFRACTIONf_dihedral_angle_d16.95242261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.190.34951420.31462684X-RAY DIFFRACTION99.72
2.19-2.240.3291290.28912657X-RAY DIFFRACTION99.89
2.24-2.290.30461460.27712671X-RAY DIFFRACTION99.89
2.29-2.350.3011500.26582646X-RAY DIFFRACTION99.86
2.35-2.410.28511360.25622687X-RAY DIFFRACTION99.82
2.41-2.490.28081250.25362680X-RAY DIFFRACTION99.93
2.49-2.570.3021540.25092664X-RAY DIFFRACTION99.79
2.57-2.660.26731530.24432664X-RAY DIFFRACTION99.82
2.66-2.760.28531400.24782694X-RAY DIFFRACTION99.89
2.76-2.890.27461400.24272689X-RAY DIFFRACTION99.93
2.89-3.040.26611210.22482711X-RAY DIFFRACTION99.82
3.04-3.230.23471300.21972691X-RAY DIFFRACTION99.96
3.23-3.480.2341150.212741X-RAY DIFFRACTION99.96
3.48-3.830.17951310.17662726X-RAY DIFFRACTION99.97
3.83-4.390.20961530.15812690X-RAY DIFFRACTION100
4.39-5.530.19251280.15832764X-RAY DIFFRACTION99.59
5.53-46.240.19691420.17052819X-RAY DIFFRACTION98.96
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)
12.08247160499-0.2167504858452.075789338620.703551392924-0.6737857611943.263186318190.114291046312-0.176978588947-0.2418396470090.1372830911580.1143289387540.01518303856780.0686782119829-0.150370408399-0.2268156760910.3730983325190.0647482019516-0.01517421390860.396526386587-0.02490801169730.33953740235614.4536032681-3.4380237019557.0641109471
22.30654375697-0.07867467638961.478554662081.405268739820.1805401075252.239771282610.0174080683644-0.104932157269-0.153354381284-0.06472932326960.1148239778960.20329017102-0.00361091228342-0.186026213333-0.1546442031550.2518871176530.02773832284310.001273395806310.27071800470.0009521381624750.34353292097-19.9244138791.3757318062618.8569720167
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 2

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11(chain 'A' and resid 21 through 401)AA - B21 - 400
22(chain 'B' and resid 18 through 401)BC - D18 - 400

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