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- PDB-8r2a: CpKRS complexed with lysine and an inhibitor -

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Basic information

Entry
Database: PDB / ID: 8r2a
TitleCpKRS complexed with lysine and an inhibitor
ComponentsLysine--tRNA ligase
KeywordsLIGASE / lysine-trna ligase / ATP binding / inhibitor
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 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDawson, A. / Baragana, B. / Caldwell, N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/S019170/1 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
DepositionNov 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 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
D: Lysine--tRNA ligase
C: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,21921
Polymers245,3204
Non-polymers2,89917
Water11,440635
1
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,9679
Polymers122,6602
Non-polymers1,3077
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Lysine--tRNA ligase
C: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,25112
Polymers122,6602
Non-polymers1,59210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.099, 118.667, 142.837
Angle α, β, γ (deg.)90.000, 90.376, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A - H / Auth seq-ID: 45 - 704 / Label seq-ID: 21

Dom-IDComponent-IDEns-ID
111
211
322
422
533
633
744
844
955
1055
1166
1266

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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Protein , 1 types, 4 molecules ADCB

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


Mass: 61329.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: CPATCC_001825 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7S7RG57, lysine-tRNA ligase

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Non-polymers , 6 types, 652 molecules

#2: Chemical
ChemComp-XLQ / 2-azanyl-4-(trifluoromethyl)-6-[[(1~{R},3~{S})-3-(trifluoromethyl)cyclohexyl]methyl]-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one


Mass: 382.304 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H16F6N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.52 Å3/Da / Density % sol: 51.19 % / 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 7.0, 30 mg/ml Reservoir: 0.2 M Li2SO4, 14-18% PEG 3350, 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: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.4→47.66 Å / Num. obs: 91915 / % possible obs: 96.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 33.59 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.102 / Χ2: 0.88 / Net I/σ(I): 8.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4619 / CC1/2: 0.809 / Rpim(I) all: 0.706 / Χ2: 0.9 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.657 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.201 / Average fsc free: 0.9392 / Average fsc work: 0.9573 / Cross valid method: FREE R-VALUE / ESU R: 0.526 / ESU R Free: 0.287
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.263 4690 5.104 %
Rwork0.2257 87198 -
all0.228 --
obs-91888 96.422 %
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: 34.464 Å2
Baniso -1Baniso -2Baniso -3
1--0.141 Å20 Å20.421 Å2
2--2.514 Å2-0 Å2
3----2.378 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16227 0 148 635 17010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01216766
X-RAY DIFFRACTIONr_bond_other_d0.0020.01615777
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.65522631
X-RAY DIFFRACTIONr_angle_other_deg0.6651.57136521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87452000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.8295.357112
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.262104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.601103013
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.3210789
X-RAY DIFFRACTIONr_chiral_restr0.0560.22417
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219214
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023778
X-RAY DIFFRACTIONr_nbd_refined0.20.23090
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.214638
X-RAY DIFFRACTIONr_nbtor_refined0.180.28005
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.28745
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2703
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0330.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1440.221
X-RAY DIFFRACTIONr_nbd_other0.2410.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2040.212
X-RAY DIFFRACTIONr_mcbond_it2.9653.4378024
X-RAY DIFFRACTIONr_mcbond_other2.9653.4378024
X-RAY DIFFRACTIONr_mcangle_it4.4396.17410016
X-RAY DIFFRACTIONr_mcangle_other4.4396.17410017
X-RAY DIFFRACTIONr_scbond_it3.3573.7228742
X-RAY DIFFRACTIONr_scbond_other3.3433.728735
X-RAY DIFFRACTIONr_scangle_it5.2676.68912615
X-RAY DIFFRACTIONr_scangle_other5.2576.68412604
X-RAY DIFFRACTIONr_lrange_it6.93732.22918377
X-RAY DIFFRACTIONr_lrange_other6.93132.24718285
X-RAY DIFFRACTIONr_ncsr_local_group_10.0330.0516799
X-RAY DIFFRACTIONr_ncsr_local_group_20.0310.0516851
X-RAY DIFFRACTIONr_ncsr_local_group_30.0350.0516800
X-RAY DIFFRACTIONr_ncsr_local_group_40.0340.0516836
X-RAY DIFFRACTIONr_ncsr_local_group_50.0340.0516800
X-RAY DIFFRACTIONr_ncsr_local_group_60.0320.0516848
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.032650.0501
12AX-RAY DIFFRACTIONLocal ncs0.032650.0501
23AX-RAY DIFFRACTIONLocal ncs0.03080.0501
24AX-RAY DIFFRACTIONLocal ncs0.03080.0501
35AX-RAY DIFFRACTIONLocal ncs0.035260.0501
36AX-RAY DIFFRACTIONLocal ncs0.035260.0501
47AX-RAY DIFFRACTIONLocal ncs0.03390.0501
48AX-RAY DIFFRACTIONLocal ncs0.03390.0501
59AX-RAY DIFFRACTIONLocal ncs0.033950.0501
510AX-RAY DIFFRACTIONLocal ncs0.033950.0501
611AX-RAY DIFFRACTIONLocal ncs0.03240.0501
612AX-RAY DIFFRACTIONLocal ncs0.03240.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.4-2.4620.5193540.46664750.46970210.8760.90397.26530.443
2.462-2.5290.5143350.43362980.43768320.880.91297.08720.4
2.529-2.6030.4093370.37460900.37666310.9090.92896.92350.34
2.603-2.6820.3853080.35456610.35564510.9110.92792.52830.318
2.682-2.770.3543250.31657810.31862520.9220.94397.66470.28
2.77-2.8670.3563180.27755920.28160550.9250.95497.60530.243
2.867-2.9750.2943030.24753590.24958450.9450.96396.86910.219
2.975-3.0960.3072670.24152150.24456340.9370.96697.30210.217
3.096-3.2330.2722820.22849570.2353940.9580.97297.12640.213
3.233-3.390.2562350.21847420.2251560.960.97796.52830.207
3.39-3.5720.2272060.21743200.21849270.9620.97791.86120.208
3.572-3.7880.2222280.19142780.19246420.9720.98497.07020.185
3.788-4.0470.2192390.1839890.18243830.9690.98496.46360.175
4.047-4.3690.1681870.14238070.14440860.9840.98997.74840.14
4.369-4.7820.1511730.12634600.12737630.9860.99196.54530.124
4.782-5.340.1961680.15730330.15934180.9790.98793.65130.153
5.34-6.1530.2081630.1928080.19130180.9750.98598.44270.182
6.153-7.5040.2271240.19924070.225740.9810.98498.32950.193
7.504-10.4840.2041000.17917890.1820170.9860.98893.65390.18
10.484-47.6570.219380.24611370.24511850.980.97299.15610.256

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