7BQW

Crystal structure of Methionine gamma-lyase from Fusobacterium nucleatum

• PDB DOI: https://doi.org/10.2210/pdb7BQW/pdb

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


• Deposited: 2020-03-25 Released: 2020-04-15 
• Deposition Author(s): Lan, J., Chen, Y., Liu, W., Xu, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Methionine gamma-lyase from Fusobacterium nucleatum

Lan, J., Liu, W., Chen, Y., Xu, 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: 173.43 kDa 
• Atom Count: 10,958 
• Modelled Residue Count: 1,415 
• Deposited Residue Count: 1,580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-methionine gamma-lyase	A, B, C, D	395	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.205	α = 90
b = 95.205	β = 90
c = 302.253	γ = 120

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: 2020-04-15 
Deposition Author(s): Lan, J., Chen, Y., Liu, W., Xu, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31200556
National Natural Science Foundation of China (NSFC)	China	21272031

Revision History  

• Version 1.0: 2020-04-15
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description