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- PDB-8s00: CpKRS complexed with lysine and an inhibitor -

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Basic information

Entry
Database: PDB / ID: 8s00
TitleCpKRS complexed with lysine and an inhibitor
ComponentsLysine--tRNA ligase
KeywordsLIGASE / Cryptosporidium / ATP binding
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 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. ...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 / 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, OB-fold
Similarity search - Domain/homology
: / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDawson, A. / Baragana, B. / Caldwell, N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MR/S01970/1 United Kingdom
CitationJournal: Sci Transl Med / Year: 2024
Title: Cryptosporidium lysyl-tRNA synthetase inhibitors define the interplay between solubility and permeability required to achieve efficacy.
Authors: Caldwell, N. / Peet, C. / Miller, P. / Colon, B.L. / Taylor, M.G. / Cocco, M. / Dawson, A. / Lukac, I. / Teixeira, J.E. / Robinson, L. / Frame, L. / Seizova, S. / Damerow, S. / Tamaki, F. / ...Authors: Caldwell, N. / Peet, C. / Miller, P. / Colon, B.L. / Taylor, M.G. / Cocco, M. / Dawson, A. / Lukac, I. / Teixeira, J.E. / Robinson, L. / Frame, L. / Seizova, S. / Damerow, S. / Tamaki, F. / Post, J. / Riley, J. / Mutter, N. / Hanna, J.C. / Ferguson, L. / Hu, X. / Tinti, M. / Forte, B. / Norcross, N.R. / Campbell, P.S. / Svensen, N. / Caldwell, F.C. / Jansen, C. / Postis, V. / Read, K.D. / Huston, C.D. / Gilbert, I.H. / Baragana, B. / Pawlowic, M.C.
History
DepositionFeb 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)124,55213
Polymers122,9182
Non-polymers1,63411
Water12,538696
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-42 kcal/mol
Surface area39280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.987, 121.761, 143.092
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 44 - 544 / Label seq-ID: 20 - 520

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#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 Iowa (eukaryote)
Gene: cgd4_2370 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5CR27, lysine-tRNA ligase

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Non-polymers , 5 types, 707 molecules

#2: Chemical ChemComp-A1H4W / 6-oxidanyl-~{N}-[(1-oxidanylcyclohexyl)methyl]-4-oxidanylidene-chromene-2-carboxamide


Mass: 317.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.59 Å3/Da / Density % sol: 52.44 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein buffer: 25 mM HEPES, 500 mM NaCl, 5% glycerol, 0.5 mM TCEP, pH 7, 30 mg/ml Reservoir: 0.2 M Li2SO4, 14-18% PEG3350, 0.1 M tris pH 7.4-7.8
PH range: 7.4-7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97627 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 2→56.08 Å / Num. obs: 86869 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 27.96 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.223 / Rpim(I) all: 0.09 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.04 Å / Redundancy: 14.1 % / Rmerge(I) obs: 2.516 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 64489 / CC1/2: 0.494 / Rpim(I) all: 1.002 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→56.08 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.204 / SU ML: 0.132 / Cross valid method: FREE R-VALUE / ESU R: 0.161 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2219 4333 4.992 %
Rwork0.1816 82460 -
all0.184 --
obs-86793 99.976 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.101 Å2
Baniso -1Baniso -2Baniso -3
1--1.821 Å20 Å20 Å2
2--2.743 Å20 Å2
3----0.922 Å2
Refinement stepCycle: LAST / Resolution: 2→56.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8118 0 92 696 8906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0128415
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167944
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.65511344
X-RAY DIFFRACTIONr_angle_other_deg0.4631.57218391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00751003
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.295.35756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39101515
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.1410395
X-RAY DIFFRACTIONr_chiral_restr0.0670.21210
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029624
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021898
X-RAY DIFFRACTIONr_nbd_refined0.2090.21544
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.27479
X-RAY DIFFRACTIONr_nbtor_refined0.1810.24057
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24369
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2675
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1780.213
X-RAY DIFFRACTIONr_nbd_other0.220.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.220
X-RAY DIFFRACTIONr_mcbond_it2.6963.3684020
X-RAY DIFFRACTIONr_mcbond_other2.6953.3674019
X-RAY DIFFRACTIONr_mcangle_it3.5886.045016
X-RAY DIFFRACTIONr_mcangle_other3.5886.045017
X-RAY DIFFRACTIONr_scbond_it3.7173.7094395
X-RAY DIFFRACTIONr_scbond_other3.7173.7094396
X-RAY DIFFRACTIONr_scangle_it5.5296.6476327
X-RAY DIFFRACTIONr_scangle_other5.5286.6476328
X-RAY DIFFRACTIONr_lrange_it6.52933.0129628
X-RAY DIFFRACTIONr_lrange_other6.49432.4499435
X-RAY DIFFRACTIONr_ncsr_local_group_10.0630.0516621
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.063060.05009
12AX-RAY DIFFRACTIONLocal ncs0.063060.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.3343040.326029X-RAY DIFFRACTION100
2.052-2.1080.3193230.3025867X-RAY DIFFRACTION100
2.108-2.1690.2923240.2715688X-RAY DIFFRACTION100
2.169-2.2360.2822840.2425538X-RAY DIFFRACTION99.9828
2.236-2.3090.2553060.2275354X-RAY DIFFRACTION99.8941
2.309-2.390.2812860.2185206X-RAY DIFFRACTION99.9818
2.39-2.480.2262710.1955038X-RAY DIFFRACTION100
2.48-2.5810.2492400.194865X-RAY DIFFRACTION99.9804
2.581-2.6950.2512400.1864673X-RAY DIFFRACTION100
2.695-2.8270.2242340.1744469X-RAY DIFFRACTION100
2.827-2.9790.2381960.174285X-RAY DIFFRACTION100
2.979-3.1590.2231980.1724045X-RAY DIFFRACTION100
3.159-3.3770.2111710.1573819X-RAY DIFFRACTION100
3.377-3.6460.2041850.1553565X-RAY DIFFRACTION100
3.646-3.9920.1961700.1613261X-RAY DIFFRACTION99.9126
3.992-4.4610.1771680.1432984X-RAY DIFFRACTION100
4.461-5.1450.1571310.1342661X-RAY DIFFRACTION100
5.145-6.2890.2241290.1752257X-RAY DIFFRACTION100
6.289-8.8380.21070.151791X-RAY DIFFRACTION100
8.838-56.080.166660.1651065X-RAY DIFFRACTION99.9117

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