9L9G | pdb_00009l9g

Crystal structure of L-threonine aldolase N18S/Q39R/Y319L triple mutant in complex with glycine from Neptunomonas marina

• PDB DOI: https://doi.org/10.2210/pdb9L9G/pdb

• Classification: LYASE
• Organism(s): Neptunomonas marina
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-12-30 Released: 2026-01-07 
• Deposition Author(s): Wu, J.Y., Liu, T.H., Yan, W.P., Feng, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 
  0.262 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of L-threonine aldolase N18S/Q39R/Y319L triple mutant in complex with glycine from Neptunomonas marina

Wu, J.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 153.27 kDa 
• Atom Count: 10,316 
• Modeled Residue Count: 1,370 
• Deposited Residue Count: 1,424 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-threonine aldolase	A, C, D	356	Neptunomonas marina	Mutation(s): 3  Gene Names: EOE65_08265 EC: 4.1.2.48
UniProt
Find proteins for A0A437Q8X1 (Neptunomonas marina) Explore A0A437Q8X1  Go to UniProtKB:  A0A437Q8X1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L-threonine aldolase	B	356	Neptunomonas marina	Mutation(s): 3  Gene Names: EOE65_08265 EC: 4.1.2.48
UniProt
Find proteins for A0A437Q8X1 (Neptunomonas marina) Explore A0A437Q8X1  Go to UniProtKB:  A0A437Q8X1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLG (Subject of Investigation/LOI)	G [auth B]	N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] C10 H15 N2 O7 P FEVQWBMNLWUBTF-UHFFFAOYSA-N
GLY (Subject of Investigation/LOI)	E [auth A], F [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free:  0.262 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 270.823	α = 90
b = 57.718	β = 105.553
c = 92.16	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-07 
Deposition Author(s): Wu, J.Y., Liu, T.H., Yan, W.P., Feng, Y.

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

Revision History  

• Version 1.0: 2026-01-07
  Type: Initial release