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- PDB-6l4q: Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falcip... -

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Basic information

Entry
Database: PDB / ID: 6l4q
TitleCrystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Clado-B
ComponentsLysine--tRNA ligase
KeywordsSTRUCTURAL PROTEIN/INHIBITOR / Cladosporin Analog / Stereochemistry / Amino-acyl tRNA synthetase / STRUCTURAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA binding / mitochondrion / extracellular space ...ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA binding / mitochondrion / extracellular space / ATP binding / nucleus / cytosol
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 / 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, 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 / 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
Chem-E5R / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBabbar, P. / Sharma, A. / Manickam, Y. / Mishra, S. / Harlos, K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR13636 India
Citation
Journal: Chembiochem / Year: 2021
Title: Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum complexed with L-lysine and Cladosporin inhibitor, Cla-B
Authors: Babbar, P. / Sato, M. / Manickam, Y. / Mishra, S. / Harlos, K. / Gupta, S. / Parvez, S. / Kikuchi, H. / Sharma, A.
#1: Journal: J. Struct. Funct. Genomics / Year: 2014
Title: Structural basis of malaria parasite lysyl-tRNA synthetase inhibition by cladosporin.
Authors: Khan, S. / Sharma, A. / Belrhali, H. / Yogavel, M. / Sharma, A.
History
DepositionOct 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 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
B: Lysine--tRNA ligase
A: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2916
Polymers117,4142
Non-polymers8774
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-47 kcal/mol
Surface area40500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.181, 121.833, 179.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 58706.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1350100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IDJ8, lysine-tRNA ligase
#2: Chemical ChemComp-E5R / (3R)-3-[[(3R)-3-methylpiperidin-1-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one


Mass: 291.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21NO4
#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Carboxylic acids-0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate Buffer System- ...Details: 0.1M Carboxylic acids-0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate Buffer System- Imidazole; MES monohydrate (acid) 50% v/v Precipitant Mix25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 293.14 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3→59.9 Å / Num. obs: 23834 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 61.172 Å2 / CC1/2: 0.982 / Net I/σ(I): 3.1
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID% possible all
3-3.0511810.2198.7
8.14-59.91134211100

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Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
PHASERphasing
DIALSdata reduction
PDB_EXTRACTdata extraction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PG3

4pg3


Resolution: 3.1→57.692 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.286 1046 4.86 %
Rwork0.2325 20468 -
obs0.2351 21514 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.2 Å2 / Biso mean: 67.3896 Å2 / Biso min: 20.71 Å2
Refinement stepCycle: final / Resolution: 3.1→57.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7937 0 62 50 8049
Biso mean--67.15 42.25 -
Num. residues----972
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.26350.39661280.3231287299
3.2635-3.46790.36131480.29162863100
3.4679-3.73560.31691690.26292873100
3.7356-4.11150.3231570.23232874100
4.1115-4.70620.24371390.19052938100
4.7062-5.92830.26351670.21882926100
5.9283-57.690.24681380.21723122100

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