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- PDB-9jkl: LYSYL-TRNA SYNTHETASE(LysRS) COMPLEXED WITH LYSINE -

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Basic information

Entry
Database: PDB / ID: 9jkl
TitleLYSYL-TRNA SYNTHETASE(LysRS) COMPLEXED WITH LYSINE
ComponentsLysine--tRNA ligase
KeywordsLIGASE / tRNA synthetase tRNA ligase Lysyl-tRNA synthetase
Function / homology
Function and homology information


catalytic activity, acting on a protein / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / transferase activity / tRNA binding / magnesium ion 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 / 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 / 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 / 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
LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJani, J. / Mochi, J. / Shah, S. / Das, A. / Patel, D. / Pananghat, G. / Pappachan, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: LYSYL-TRNA SYNTHETASE(LysRS) COMPLEXED WITH LYSINE
Authors: Jani, J. / Mochi, J. / Shah, S. / Das, A. / Patel, D. / Pananghat, G. / Pappachan, A.
History
DepositionSep 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6369
Polymers59,8441
Non-polymers7928
Water7,026390
1
A: Lysine--tRNA ligase
hetero molecules

A: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,27318
Polymers119,6892
Non-polymers1,58416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area12320 Å2
ΔGint-42 kcal/mol
Surface area39610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.015, 105.015, 241.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 59844.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: lysS, SAV0517 / Production host: Escherichia coli (E. coli) / References: UniProt: P67609, lysine-tRNA ligase
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 5.56 Å3/Da / Density % sol: 77.88 %
Crystal growTemperature: 296 K / Method: microbatch / Details: 0.1M Tris HCl pH 8.5, 8% W/V PEG 8000, 5mM Lysine

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2022
RadiationMonochromator: Double Crystal Si111 with LN2 closed loop cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→79.22 Å / Num. obs: 60972 / % possible obs: 100 % / Redundancy: 24.8 % / Biso Wilson estimate: 47.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.028 / Rrim(I) all: 0.141 / Χ2: 1 / Net I/σ(I): 16.9
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 25.2 % / Rmerge(I) obs: 1.524 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4444 / CC1/2: 0.959 / Rpim(I) all: 0.309 / Rrim(I) all: 1.556 / Χ2: 1.04 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Cootmodel building
DIALSdata collection
Aimlessdata scaling
PHASERphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→79.22 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.228 3070 -
Rwork0.204 --
obs-60972 100 %
Refinement stepCycle: LAST / Resolution: 2.3→79.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3927 0 52 390 4369
LS refinement shellResolution: 2.3→2.36 Å
RfactorNum. reflection% reflection
Rfree0.2286 --
Rwork0.2046 --
obs-4444 100 %

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