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

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Basic information

Entry
Database: PDB / ID: 6kct
TitleCrystal structure of plasmodium lysyl-tRNA synthetase in complex with a cladosporin derivative 5
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, N-terminal / Lysine-tRNA ligase, class II / 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, N-terminal / Lysine-tRNA ligase, class II / 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-D5O / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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 29, 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)240,81112
Polymers239,1254
Non-polymers1,6868
Water1,44180
1
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,4056
Polymers119,5622
Non-polymers8434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-44 kcal/mol
Surface area39380 Å2
MethodPISA
2
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,4056
Polymers119,5622
Non-polymers8434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-45 kcal/mol
Surface area39400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.112, 89.703, 100.049
Angle α, β, γ (deg.)76.760, 72.800, 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-D5O / 3-(cyclohexylmethyl)-6,8-bis(oxidanyl)isochromen-1-one


Mass: 274.312 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H18O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C6H15N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
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: 3.25→50 Å / Num. obs: 33930 / % possible obs: 94.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 58.99 Å2 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.159 / Rrim(I) all: 0.297 / Χ2: 1.04 / Net I/σ(I): 2.6 / Num. measured all: 121802
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.25-3.373.50.71834460.8210.440.8440.53595.9
3.37-3.53.50.43734460.940.2950.531.48596.4
3.5-3.663.60.48234630.9630.3020.5710.89597.2
3.66-3.853.60.37335020.9830.2420.4461.06396.7
3.85-4.093.50.29834050.9580.2050.3641.47895.2
4.09-4.413.60.22633440.970.1360.2640.9993.6
4.41-4.853.40.18730580.970.1150.221.0886.1
4.85-5.563.70.17135440.9780.1020.1990.90297.8
5.56-73.70.17334460.9680.1020.2010.7996.3
7-503.60.10932760.9760.0660.1271.24191.6

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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: 3.25→48.946 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 38.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3116 1637 4.88 %
Rwork0.2922 31921 -
obs0.2931 33558 93.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.66 Å2 / Biso mean: 60.8876 Å2 / Biso min: 33.27 Å2
Refinement stepCycle: final / Resolution: 3.25→48.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15628 0 80 80 15788
Biso mean--48.18 41.8 -
Num. residues----2013
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 (%)
3.2502-3.36640.38081450.34073169331492
3.3664-3.50110.42311590.40633152331193
3.5011-3.66040.34281880.33383284347297
3.6604-3.85330.39661830.36743311349496
3.8533-4.09460.4271610.36553152331393
4.0946-4.41060.30371580.25823197335593
4.4106-4.85410.25591660.25392880304686
4.8541-5.55560.25761700.2533397356798
5.5556-6.99630.2911730.27523283345696
6.9963-48.9520.21421340.22283096323090
Refinement TLS params.Method: refined / Origin x: 1.496 Å / Origin y: 13.1431 Å / Origin z: 22.7805 Å
111213212223313233
T0.2576 Å2-0.0063 Å20.0257 Å2-0.5214 Å20.0453 Å2--0.4951 Å2
L0.0194 °20.0401 °20.0965 °2-0.2941 °20.2005 °2--0.5075 °2
S-0.0114 Å °-0.0621 Å °-0.0381 Å °-0.0188 Å °0.012 Å °0.0571 Å °-0.0551 Å °-0.0473 Å °0.0053 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA78 - 583
2X-RAY DIFFRACTION1allB79 - 582
3X-RAY DIFFRACTION1allC78 - 582
4X-RAY DIFFRACTION1allD78 - 582
5X-RAY DIFFRACTION1allS6 - 981
6X-RAY DIFFRACTION1allF1 - 4
7X-RAY DIFFRACTION1allK1 - 4

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