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- PDB-6hcu: Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falcip... -

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Basic information

Entry
Database: PDB / ID: 6hcu
TitleCrystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum bound to a difluoro cyclohexyl chromone ligand
ComponentsLysine--tRNA ligase
KeywordsTRANSFERASE / ADENYLYLTRANSFERASE ACTIVITY / TRNA BINDING / LIGASE
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / tRNA binding / ATP binding / cytosol
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / 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) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-FYB / HISTIDINE / LYSINE / DI(HYDROXYETHYL)ETHER / Lysine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsTamjar, J. / Robinson, D.A. / Baragana, B. / Norcross, N. / Forte, B. / Walpole, C. / Gilbert, I.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1032548 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis.
Authors: Baragana, B. / Forte, B. / Choi, R. / Nakazawa Hewitt, S. / Bueren-Calabuig, J.A. / Pisco, J.P. / Peet, C. / Dranow, D.M. / Robinson, D.A. / Jansen, C. / Norcross, N.R. / Vinayak, S. / ...Authors: Baragana, B. / Forte, B. / Choi, R. / Nakazawa Hewitt, S. / Bueren-Calabuig, J.A. / Pisco, J.P. / Peet, C. / Dranow, D.M. / Robinson, D.A. / Jansen, C. / Norcross, N.R. / Vinayak, S. / Anderson, M. / Brooks, C.F. / Cooper, C.A. / Damerow, S. / Delves, M. / Dowers, K. / Duffy, J. / Edwards, T.E. / Hallyburton, I. / Horst, B.G. / Hulverson, M.A. / Ferguson, L. / Jimenez-Diaz, M.B. / Jumani, R.S. / Lorimer, D.D. / Love, M.S. / Maher, S. / Matthews, H. / McNamara, C.W. / Miller, P. / O'Neill, S. / Ojo, K.K. / Osuna-Cabello, M. / Pinto, E. / Post, J. / Riley, J. / Rottmann, M. / Sanz, L.M. / Scullion, P. / Sharma, A. / Shepherd, S.M. / Shishikura, Y. / Simeons, F.R.C. / Stebbins, E.E. / Stojanovski, L. / Straschil, U. / Tamaki, F.K. / Tamjar, J. / Torrie, L.S. / Vantaux, A. / Witkowski, B. / Wittlin, S. / Yogavel, M. / Zuccotto, F. / Angulo-Barturen, I. / Sinden, R. / Baum, J. / Gamo, F.J. / Maser, P. / Kyle, D.E. / Winzeler, E.A. / Myler, P.J. / Wyatt, P.G. / Floyd, D. / Matthews, D. / Sharma, A. / Striepen, B. / Huston, C.D. / Gray, D.W. / Fairlamb, A.H. / Pisliakov, A.V. / Walpole, C. / Read, K.D. / Van Voorhis, W.C. / Gilbert, I.H.
History
DepositionAug 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)119,02311
Polymers117,4142
Non-polymers1,6099
Water17,402966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint-20 kcal/mol
Surface area39870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.137, 95.344, 166.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lysine--tRNA ligase / Lysyl-tRNA synthetase


Mass: 58706.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1350100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IDJ8, lysine-tRNA ligase

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Non-polymers , 6 types, 975 molecules

#2: Chemical ChemComp-FYB / ~{N}-[[4,4-bis(fluoranyl)-1-oxidanyl-cyclohexyl]methyl]-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide


Mass: 355.308 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16F3NO4
#3: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-HIS / HISTIDINE / Histidine


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#6: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 966 / 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: 2.14 Å3/Da / Density % sol: 42.64 % / Description: Plate
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 2 % (v/v) Tascimate pH 6.0, 20 % (w/v) PEG 3350
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.074 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.074 Å / Relative weight: 1
ReflectionResolution: 1.62→83 Å / Num. obs: 148069 / % possible obs: 99.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 10
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.59 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H02

4h02


Resolution: 1.62→82.74 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.298 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.095
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 7280 4.9 %RANDOM
Rwork0.1827 ---
obs0.1848 139948 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.21 Å2 / Biso mean: 25.892 Å2 / Biso min: 7.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--0.53 Å20 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 1.62→82.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7860 0 107 966 8933
Biso mean--29.29 37.03 -
Num. residues----970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0198322
X-RAY DIFFRACTIONr_bond_other_d0.0030.027708
X-RAY DIFFRACTIONr_angle_refined_deg2.2451.97611280
X-RAY DIFFRACTIONr_angle_other_deg1.181317970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16851012
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03524.296398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.301151472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9961543
X-RAY DIFFRACTIONr_chiral_restr0.1520.21220
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0219089
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021694
LS refinement shellResolution: 1.619→1.662 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 501 -
Rwork0.338 10058 -
all-10559 -
obs--97.4 %

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