9GJ9 | pdb_00009gj9

Crystal structure of methionine gamma-lyase from Brevibacterium sandarakinum in complex with PLP and norleucine at pH 6.5

• PDB DOI: https://doi.org/10.2210/pdb9GJ9/pdb

• Classification: LYASE
• Organism(s): Brevibacterium sandarakinum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-21 Released: 2025-09-03 
• Deposition Author(s): Kopecny, D., Ferchaud, N., Briozzo, P.
• Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic, Other government, Other private, Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.287 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Starting Model: in silico

Literature

Functional and structural characterization of methionine gamma-lyases from Brevibacterium bacteria: insights into cofactor retention.

Ferchaud, N., Boyer, A., Odegard, B., Hentati, S., Simonson, T., Machover, D., Kopecny, D., Briozzo, P.

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)

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 259.58 kDa 
• Atom Count: 16,999 
• Modeled Residue Count: 2,308 
• Deposited Residue Count: 2,478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine gamma-synthase	A, B, C, D, E, F	413	Brevibacterium sandarakinum	Mutation(s): 0  Gene Names: SAMN04489751_4033 EC: 4.4.1.11 (PDB Primary Data), 4.4.1.2 (UniProt)
UniProt
Find proteins for A0A1H1YBL2 (Brevibacterium sandarakinum) Explore A0A1H1YBL2  Go to UniProtKB:  A0A1H1YBL2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NLE (Subject of Investigation/LOI)	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	NORLEUCINE C6 H13 N O2 LRQKBLKVPFOOQJ-YFKPBYRVSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.287 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.574	α = 90
b = 229.734	β = 90
c = 155.174	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
autoPROC	data processing
autoPROC	data reduction
Aimless	data scaling
STARANISO	data scaling
PHASER	phasing
BUSTER	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Kopecny, D., Ferchaud, N., Briozzo, P.

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Funding Organization	Location	Grant Number
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	8J23FR011 MOBILITY
Other government	France	FR 49271QH BARRANDE
Other private	France	IMEBATRACA
Agence Nationale de la Recherche (ANR)	France	ANR-11-IDEX-0003, Jean d'Alembert fellowship

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release