9HEE | pdb_00009hee

Crystal structure of methionine gamma-lyase from Brevibacterium aurantiacum having disordered N-terminus and devoid of PLP cofactor

• PDB DOI: https://doi.org/10.2210/pdb9HEE/pdb

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


• Deposited: 2024-11-13 Released: 2025-10-22 
• 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: 3.24 Å
• R-Value Free: 
  0.284 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

Literature

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

Ferchaud, N., Boyer, A., Odegard, B., Hentati, S., Machover, 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

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: 342.56 kDa 
• Atom Count: 18,176 
• Modeled Residue Count: 2,512 
• Deposited Residue Count: 3,304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine gamma-synthase	A, B, C, D, E, F, G, H	413	Brevibacterium aurantiacum	Mutation(s): 0  Gene Names: BAUR9175_03070, BAUR920_03040, BAURA63_02933, BAURA86_00394 EC: 4.4.1.11 (PDB Primary Data), 4.4.1.2 (UniProt)
UniProt
Find proteins for A0A2H1K3G9 (Brevibacterium aurantiacum) Explore A0A2H1K3G9  Go to UniProtKB:  A0A2H1K3G9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free:  0.284 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.848	α = 90
b = 165.848	β = 90
c = 209.263	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
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	MOBILITY 8J23FR011
Other government	France	FR 49271QH PHC BARRANDE
Other private	France	IMEBATRACA
Agence Nationale de la Recherche (ANR)	France	France 2023 ANR-11-IDEX-0003, Jean d'Alembert fellowship at Paris-Saclay

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release