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

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Basic information

Entry
Database: PDB / ID: 6kbf
TitleCrystal structure of plasmodium lysyl-tRNA synthetase in complex with a cladosporin derivative 3
ComponentsLysine--tRNA ligase
KeywordsLIGASE / Inhibitor / Complex
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / nucleic acid binding / ATP binding / cytoplasm
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-D4X / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 24, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,97412
Polymers119,5622
Non-polymers1,41210
Water11,890660
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-43 kcal/mol
Surface area39050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.932, 70.822, 101.125
Angle α, β, γ (deg.)90.000, 111.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 59781.133 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 670 molecules

#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-D4X / (3~{S})-3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)-3,4-dihydro-2~{H}-isoquinolin-1-one


Mass: 289.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23NO3 / Feature type: SUBJECT OF INVESTIGATION
#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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.82 %
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: Apr 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.92→47.07 Å / Num. obs: 87690 / % possible obs: 99.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 29.83 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
1.92-1.975.31.3135919191.7
8.59-47.076.10.041034198.2

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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: 1.92→43.845 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2161 4255 4.86 %
Rwork0.1802 83352 -
obs0.182 87607 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.38 Å2 / Biso mean: 44.9515 Å2 / Biso min: 15.78 Å2
Refinement stepCycle: final / Resolution: 1.92→43.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7903 0 96 660 8659
Biso mean--39.35 47.82 -
Num. residues----1007
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 (%)
1.92-1.98860.30184210.27827678809992
1.9886-2.06830.31254090.250684088817100
2.0683-2.16240.27414310.229683598790100
2.1624-2.27640.25694370.20983628799100
2.2764-2.4190.24864030.199184018804100
2.419-2.60580.24194260.189883918817100
2.6058-2.8680.2254220.181983718793100
2.868-3.28280.214360.176584208856100
3.2828-4.13550.18664540.157984058859100
4.1355-43.85690.18394160.15638557897399
Refinement TLS params.Method: refined / Origin x: -50.908 Å / Origin y: -8.8197 Å / Origin z: 23.3897 Å
111213212223313233
T0.2685 Å2-0.0264 Å20.0947 Å2-0.2186 Å2-0.0027 Å2--0.2575 Å2
L0.5753 °2-0.1843 °20.2809 °2-1.1801 °2-0.1825 °2--1.1873 °2
S0.0249 Å °0.0231 Å °0.0466 Å °-0.3934 Å °-0.043 Å °-0.2879 Å °0.0811 Å °0.1798 Å °-0.0154 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA79 - 582
2X-RAY DIFFRACTION1allB79 - 581
3X-RAY DIFFRACTION1allK1 - 2
4X-RAY DIFFRACTION1allC1 - 2
5X-RAY DIFFRACTION1allD1 - 2
6X-RAY DIFFRACTION1allD3 - 5
7X-RAY DIFFRACTION1allF1 - 922
8X-RAY DIFFRACTION1allE1

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