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- PDB-6hcw: Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium p... -

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Basic information

Entry
Database: PDB / ID: 6hcw
TitleCrystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-lysine and 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 / tRNA binding / ATP binding / membrane / cytosol
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / 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 / Lysine-tRNA ligase, class II, N-terminal / 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 / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsRobinson, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)124,0457
Polymers122,9182
Non-polymers1,1275
Water16,340907
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-47 kcal/mol
Surface area39000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.514, 142.650, 72.939
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 61459.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (strain Iowa II) (eukaryote)
Gene: cgd4_2370 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5CR27, lysine-tRNA ligase
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: 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
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 907 / 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: 2.63 Å3/Da / Density % sol: 53.15 % / Description: cuboid
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris HCl pH 8.5
PH range: 7.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.46→73 Å / Num. obs: 205432 / % possible obs: 97.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 10
Reflection shellResolution: 1.46→1.5 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.56 / % possible all: 80.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ELN

5eln


Resolution: 1.46→72.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.397 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.069
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 10237 5 %RANDOM
Rwork0.1872 ---
obs0.1886 194182 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 126.49 Å2 / Biso mean: 15.952 Å2 / Biso min: 5.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2---0.19 Å20 Å2
3----0.51 Å2
Refinement stepCycle: final / Resolution: 1.46→72.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8023 0 78 907 9008
Biso mean--9.56 24.71 -
Num. residues----997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198300
X-RAY DIFFRACTIONr_bond_other_d0.0020.027687
X-RAY DIFFRACTIONr_angle_refined_deg1.9291.97211202
X-RAY DIFFRACTIONr_angle_other_deg1.065317878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7165996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96823.902387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.684151484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.521550
X-RAY DIFFRACTIONr_chiral_restr0.1240.21199
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0219217
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021709
LS refinement shellResolution: 1.46→1.498 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 593 -
Rwork0.36 11641 -
all-12234 -
obs--79.49 %

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