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- PDB-5zh3: CRYSTAL STRUCTURE OF PfKRS WITH INHIBITOR CLADO-6 -

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Basic information

Entry
Database: PDB / ID: 5zh3
TitleCRYSTAL STRUCTURE OF PfKRS WITH INHIBITOR CLADO-6
ComponentsLysine-tRNA ligaseLysine—tRNA ligase
KeywordsLIGASE/LIGASE INHIBITOR / KRS / LIGASE-LIGASE 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-9CF / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum NF54 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsBabbar, P. / Malhotra, N. / Sharma, M. / Harlos, K. / Reddy, D.S. / Manickam, Y. / Sharma, A.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Specific Stereoisomeric Conformations Determine the Drug Potency of Cladosporin Scaffold against Malarial Parasite
Authors: Das, P. / Babbar, P. / Malhotra, N. / Sharma, M. / Jachak, G.R. / Gonnade, R.G. / Shanmugam, D. / Harlos, K. / Yogavel, M. / Sharma, A. / Reddy, D.S.
History
DepositionMar 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

Downloads & links

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Assembly

Deposited unit
A: Lysine-tRNA ligase
B: Lysine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2936
Polymers117,4142
Non-polymers8794
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-47 kcal/mol
Surface area38670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.440, 130.770, 174.700
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 / Lysine—tRNA ligase / Lysyl-tRNA synthetase


Mass: 58706.934 Da / Num. of mol.: 2 / Fragment: UNP residues 15-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum NF54 (eukaryote) / Gene: PFNF54_04763 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: W7JP72, lysine-tRNA ligase
#2: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-9CF / (3S)-6,8-dihydroxy-3-{[(2R,6R)-6-methyloxan-2-yl]methyl}-3,4-dihydro-1H-2-benzopyran-1-one


Mass: 292.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20O5

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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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.10M Carboxylic Acids, 0.1M Sodium HEPES/MOPS, 25%(v/v) MPD; 25% PEG 1000; 25%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.86→53.2 Å / Num. obs: 29117 / % possible obs: 99.8 % / Redundancy: 12.9 % / CC1/2: 0.9991 / Net I/σ(I): 13.1
Reflection shellResolution: 2.86→2.91 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1428 / CC1/2: 0.8178 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PG3

4pg3


Resolution: 2.86→53.2 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.909 / SU B: 17.779 / SU ML: 0.348 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.099 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3113 1418 4.9 %RANDOM
Rwork0.2511 ---
obs0.2541 27629 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 200.17 Å2 / Biso mean: 102.669 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-157.06 Å20 Å20 Å2
2---66.54 Å2-0 Å2
3----90.52 Å2
Refinement stepCycle: final / Resolution: 2.86→53.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7249 0 62 0 7311
Biso mean--89.66 --
Num. residues----943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197581
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.96810300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8975937
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09124.076341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.875151167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5281536
X-RAY DIFFRACTIONr_chiral_restr0.0820.21147
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215820
LS refinement shellResolution: 2.86→2.934 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 105 -
Rwork0.434 1983 -
all-2088 -
obs--99.43 %

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