8IRK

Carbon Sulfoxide lyase

• PDB DOI: https://doi.org/10.2210/pdb8IRK/pdb

• Classification: LYASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-18 Released: 2024-03-06 
• Deposition Author(s): Gong, W.M., Wei, L.L., Liu, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Israel Ministry of Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.246 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Structure of Mycobacterial ergothioneine-biosynthesis C-S lyase EgtE

Gong, W.M., Wei, L.L., Liu, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 166.59 kDa 
• Atom Count: 11,429 
• Modelled Residue Count: 1,500 
• Deposited Residue Count: 1,568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable hercynylcysteine sulfoxide lyase	A, B, C, D	392	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: egtE, MSMEG_6246, MSMEI_6085 EC: 4.4
UniProt
Find proteins for A0R5M7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R5M7  Go to UniProtKB:  A0R5M7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	E [auth A], G [auth B], H [auth C], I [auth D]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PYR (Subject of Investigation/LOI)	F [auth A]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.246 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.314	α = 110.77
b = 90.372	β = 105.95
c = 101.531	γ = 103.07

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Gong, W.M., Wei, L.L., Liu, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--
Israel Ministry of Science and Technology	Israel	--

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release