9JKL | pdb_00009jkl

LYSYL-TRNA SYNTHETASE(LysRS) COMPLEXED WITH LYSINE

• PDB DOI: https://doi.org/10.2210/pdb9JKL/pdb

• Classification: LIGASE
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-16 Released: 2025-09-10 
• Deposition Author(s): Jani, J., Mochi, J., Shah, S., Das, A., Patel, D., Pananghat, G., Pappachan, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.228 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.191 (DCC) 

Starting Model: in silico

Literature

LYSYL-TRNA SYNTHETASE(LysRS) COMPLEXED WITH LYSINE

Jani, J., Mochi, J., Shah, S., Das, A., Patel, D., Pananghat, G., Pappachan, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 60.64 kDa 
• Atom Count: 4,394 
• Modeled Residue Count: 488 
• Deposited Residue Count: 523 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase	A	523	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: lysS, SAV0517 EC: 6.1.1.6
UniProt
Find proteins for P67609 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore P67609  Go to UniProtKB:  P67609

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LYS (Subject of Investigation/LOI)	B [auth A]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
GOL (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.228 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.191 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.015	α = 90
b = 105.015	β = 90
c = 241.35	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
DIALS	data collection
Aimless	data scaling
PHASER	phasing
MOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Jani, J., Mochi, J., Shah, S., Das, A., Patel, D., Pananghat, G., Pappachan, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release