6LXU

Crystal structure of methionine gamma-lyase from Fusobacterium nucleatum

• PDB DOI: https://doi.org/10.2210/pdb6LXU/pdb

• Classification: LYASE
• Organism(s): Fusobacterium nucleatum subsp. nucleatum ATCC 25586
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-02-12 Released: 2021-02-17 
• Deposition Author(s): Kezuka, Y., Yoshida, Y., Nonaka, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.161 
• R-Value Work: 0.152 
• R-Value Observed: 0.152 

Starting Model: experimental

Literature

Crystal structure of methionine gamma-lyase from Fusobacterium nucleatum

Kezuka, 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 44.11 kDa 
• Atom Count: 3,441 
• Modelled Residue Count: 391 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-methionine gamma-lyase	A	398	Fusobacterium nucleatum subsp. nucleatum ATCC 25586	Mutation(s): 0  Gene Names: FN1419 EC: 4.4.1.11 (PDB Primary Data), 4.4.1.2 (PDB Primary Data), 4.4.1.28 (PDB Primary Data)
UniProt
Find proteins for Q8RDT4 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8RDT4  Go to UniProtKB:  Q8RDT4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD (Subject of Investigation/LOI)	B [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
NO3 (Subject of Investigation/LOI)	C [auth A], D [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.161 
• R-Value Work: 0.152 
• R-Value Observed: 0.152 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.947	α = 90
b = 99.915	β = 90
c = 138.297	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Kezuka, Y., Yoshida, Y., Nonaka, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP25462897
Japan Society for the Promotion of Science (JSPS)	Japan	JP23792130

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description