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- PDB-6kcn: Crystal structure of plasmodium lysyl-tRNA synthetase in complex ... -

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Basic information

Entry
Database: PDB / ID: 6kcn
TitleCrystal structure of plasmodium lysyl-tRNA synthetase in complex with a cladosporin derivative 4
ComponentsLysine--tRNA ligase
KeywordsLIGASE / Inhibitor / Complex
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / ATP binding / 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-D5F / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhou, J. / Fang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)21778064 China
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Atomic Resolution Analyses of Isocoumarin Derivatives for Inhibition of Lysyl-tRNA Synthetase.
Authors: Zhou, J. / Zheng, L. / Hei, Z. / Li, W. / Wang, J. / Yu, B. / Fang, P.
History
DepositionJun 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: 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
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,23516
Polymers239,1254
Non-polymers2,11112
Water15,853880
1
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,6188
Polymers119,5622
Non-polymers1,0556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-47 kcal/mol
Surface area39330 Å2
MethodPISA
2
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,6188
Polymers119,5622
Non-polymers1,0556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-47 kcal/mol
Surface area38990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.174, 89.920, 100.044
Angle α, β, γ (deg.)76.700, 72.950, 80.110
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 59781.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate NF54) (eukaryote)
Strain: isolate NF54 / Gene: PFNF54_04763 / Production host: Escherichia coli (E. coli) / References: UniProt: W7JP72, lysine-tRNA ligase
#2: Chemical
ChemComp-D5F / 3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)isochromen-1-one


Mass: 288.338 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H20O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 880 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: tri-sodium citrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 107713 / % possible obs: 92 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.15 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.065 / Rrim(I) all: 0.124 / Χ2: 0.831 / Net I/σ(I): 4.5 / Num. measured all: 361081
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.283.20.506111520.6140.3310.6080.60195
2.28-2.373.20.4110150.820.2610.480.57694
2.37-2.483.20.345105000.8610.2240.4130.64390.3
2.48-2.613.30.281106510.8950.1790.3340.73391
2.61-2.773.40.234109880.9220.1480.2780.80193.6
2.77-2.993.40.175108600.9530.1090.2070.94292.7
2.99-3.293.40.135101350.9650.0850.161.1186.7
3.29-3.763.50.095108430.9770.0590.1121.14392.6
3.76-4.743.40.063105980.990.0390.0741.03290.4
4.74-503.60.047109710.9950.0280.0550.68394

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YCV

4ycv


Resolution: 2.2→49.057 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 24.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 5310 4.96 %
Rwork0.1883 101803 -
obs0.1905 107113 91.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.75 Å2 / Biso mean: 38.1027 Å2 / Biso min: 19.18 Å2
Refinement stepCycle: final / Resolution: 2.2→49.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15820 0 108 880 16808
Biso mean--30.07 38.84 -
Num. residues----2002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.27860.28845640.2347104991106395
2.2786-2.36990.27035430.2221104251096894
2.3699-2.47770.2945110.226199321044390
2.4777-2.60840.28525190.2227101051062491
2.6084-2.77180.27425120.2175103811089394
2.7718-2.98570.25865880.2079102111079993
2.9857-3.28620.24395300.193995661009687
3.2862-3.76150.235290.1788102501077993
3.7615-4.73850.17855170.1496100191053690
4.7385-49.06950.20424970.1736104151091294
Refinement TLS params.Method: refined / Origin x: 1.4697 Å / Origin y: 13.0838 Å / Origin z: 22.8897 Å
111213212223313233
T0.1952 Å2-0.0067 Å20.0196 Å2-0.2381 Å20.0294 Å2--0.2884 Å2
L0.0551 °20.037 °20.0475 °2-0.1531 °20.1076 °2--0.276 °2
S0.0095 Å °0.0003 Å °-0.0014 Å °-0.0132 Å °0.0066 Å °0.0115 Å °-0.0241 Å °-0.0054 Å °-0.0134 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA78 - 582
2X-RAY DIFFRACTION1allB79 - 582
3X-RAY DIFFRACTION1allC78 - 582
4X-RAY DIFFRACTION1allD78 - 582
5X-RAY DIFFRACTION1allE1 - 4
6X-RAY DIFFRACTION1allF1 - 917
7X-RAY DIFFRACTION1allG1 - 3
8X-RAY DIFFRACTION1allG4
9X-RAY DIFFRACTION1allK1 - 4

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