8WKR

Crystal structure of O-acetylhomoserine sulfhydrylase from Lactobacillus plantarum in the open form

• PDB DOI: https://doi.org/10.2210/pdb8WKR/pdb

• Classification: LYASE
• Organism(s): Lactiplantibacillus plantarum JDM1
• Expression System: Escherichia coli B
• Mutation(s): No 


• Deposited: 2023-09-28 Released: 2024-02-14 
• Deposition Author(s): Oda, K., Matoba, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.196 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 

Literature

Allosteric regulation of an acidophilic O-acetylhomoserine sulfhydrylase from Lactobacillus plantarum

Matoba, Y., Oda, K., Wataeda, M., Matsuo, K.

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: 193.78 kDa 
• Atom Count: 13,526 
• Modelled Residue Count: 1,616 
• Deposited Residue Count: 1,792 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-methionine gamma-lyase	A, B, C, D	448	Lactiplantibacillus plantarum JDM1	Mutation(s): 0  Gene Names: mgl
UniProt
Find proteins for A0A0G9F7S9 (Lactiplantibacillus plantarum) Explore A0A0G9F7S9  Go to UniProtKB:  A0A0G9F7S9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LLP	E [auth A], G [auth B], H [auth C], J [auth D]	(2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid C14 H22 N3 O7 P YQSOQJORMNSDJL-QFULYMJESA-N
PRO	F [auth B], I [auth D]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.196 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.281	α = 90
b = 114.929	β = 110.28
c = 98.911	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-14 
Deposition Author(s): Oda, K., Matoba, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-02-14
  Type: Initial release