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- PDB-6ka6: Crystal structure of plasmodium lysyl-tRNA synthetase in complex ... -

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Basic information

Entry
Database: PDB / ID: 6ka6
TitleCrystal structure of plasmodium lysyl-tRNA synthetase in complex with a cladosporin derivative 1
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-D4O / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.891 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 21, 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)241,24316
Polymers239,1254
Non-polymers2,11912
Water27,0411501
1
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,7149
Polymers119,5622
Non-polymers1,1517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10000 Å2
ΔGint-43 kcal/mol
Surface area39110 Å2
MethodPISA
2
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5297
Polymers119,5622
Non-polymers9675
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9340 Å2
ΔGint-45 kcal/mol
Surface area38710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.479, 90.202, 100.720
Angle α, β, γ (deg.)76.700, 72.910, 80.030
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-D4O / (3~{S})-3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one


Mass: 290.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H22O4 / 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: isolated from a natural source / Formula: C6H15N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1501 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
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: 0.97853 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.89→38.68 Å / Num. obs: 164813 / % possible obs: 88.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.25 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
1.89-1.943.40.8257979157.8
8.45-38.683.60.131874189.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YCV

4ycv


Resolution: 1.891→32.597 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 26.85
RfactorNum. reflection% reflection
Rfree0.2265 8283 5.03 %
Rwork0.1914 --
obs0.1931 164560 88.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.11 Å2 / Biso mean: 33.6835 Å2 / Biso min: 14.73 Å2
Refinement stepCycle: final / Resolution: 1.891→32.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15640 0 108 1502 17250
Biso mean--28.02 41.02 -
Num. residues----1982
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 (%)
1.8906-1.95810.31845170.2714103711088858
1.9581-2.03650.28938160.2399147981561484
2.0365-2.12920.27618940.2244165931748794
2.1292-2.24140.2649220.2151165321745493
2.2414-2.38180.26628780.2039161051698391
2.3818-2.56570.258700.2055166631753394
2.5657-2.82370.24368280.2058160931692191
2.8237-3.2320.22948580.1962165571741594
3.232-4.07070.19538440.1694162931713792
4.0707-32.60160.18538560.1654162721712892
Refinement TLS params.Method: refined / Origin x: 1.5933 Å / Origin y: 12.9705 Å / Origin z: 23.0346 Å
111213212223313233
T0.1226 Å20.0048 Å20.0133 Å2-0.1806 Å20.0488 Å2--0.2384 Å2
L0.0652 °20.0507 °20.048 °2-0.1014 °20.116 °2--0.2841 °2
S0.0113 Å °-0.0065 Å °-0.0075 Å °-0.0126 Å °0.0065 Å °0.0095 Å °-0.021 Å °-0.0007 Å °-0.0146 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA78 - 582
2X-RAY DIFFRACTION1allB79 - 582
3X-RAY DIFFRACTION1allC79 - 582
4X-RAY DIFFRACTION1allD79 - 581
5X-RAY DIFFRACTION1allS1 - 1869
6X-RAY DIFFRACTION1allE1 - 4
7X-RAY DIFFRACTION1allF1 - 4
8X-RAY DIFFRACTION1allK1 - 4

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