9KWD | pdb_00009kwd

Crystal structure of E.coli LysU complexing with LysSA and ATP

• PDB DOI: https://doi.org/10.2210/pdb9KWD/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-12-05 Released: 2025-12-10 
• Deposition Author(s): Xia, M., Hei, Z., Fang, P.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.49 Å
• R-Value Free: 
  0.254 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of E.coli LysU complexing with LysSA and ATP

Xia, M., Hei, Z., Fang, P.

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)

Macromolecule Content 

• Total Structure Weight: 59.18 kDa 
• Atom Count: 3,974 
• Modeled Residue Count: 489 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase, heat inducible	A	504	Escherichia coli K-12	Mutation(s): 0  Gene Names: lysU, b4129, JW4090 EC: 6.1.1.6
UniProt
Find proteins for P0A8N5 (Escherichia coli (strain K12)) Explore P0A8N5  Go to UniProtKB:  P0A8N5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
KAA (Subject of Investigation/LOI)	G [auth A]	5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE C16 H26 N8 O7 S NARKTLKJPPMFJF-LEJQEAHTSA-N
PEG	C [auth A], D [auth A], E [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.49 Å
• R-Value Free:  0.254 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.849	α = 90
b = 146.849	β = 90
c = 182.025	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Xia, M., Hei, Z., Fang, P.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release