6KU1

The structure of EanB/Y353A complex with ergothioneine

• PDB DOI: https://doi.org/10.2210/pdb6KU1/pdb

• Classification: TRANSFERASE
• Organism(s): Chlorobium limicola
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2019-08-30 Released: 2020-08-26 
• Deposition Author(s): Wu, L., Liu, P.H., Zhou, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.214 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Literature

Single-Step Replacement of an Unreactive C-H Bond by a C-S Bond Using Polysulfide as the Direct Sulfur Source in the Anaerobic Ergothioneine Biosynthesis

Cheng, R., Wu, L., Lai, R., Peng, C., Naowarojna, N., Hu, W., Li, X., Whelan, S.A., Lee, N., Lopez, J., Zhao, C., Yong, Y., Xue, J., Jiang, X., Grinstaff, M.W., Deng, Z., Chen, J., Cui, Q., Zhou, J.H., Liu, P.

(2020) ACS Catal 10: 8981-8994

• DOI: https://doi.org/10.1021/acscatal.0c01809

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 105.3 kDa 
• Atom Count: 7,229 
• Modelled Residue Count: 852 
• Deposited Residue Count: 920 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfurtransferase	A, B	460	Chlorobium limicola	Mutation(s): 1  Gene Names: Clim_1149
UniProt
Find proteins for B3ECE3 (Chlorobium limicola (strain DSM 245 / NBRC 103803 / 6330)) Explore B3ECE3  Go to UniProtKB:  B3ECE3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LW8 (Subject of Investigation/LOI)	E [auth A], L [auth B]	trimethyl-[(2S)-1-oxidanyl-1-oxidanylidene-3-(2-sulfanylidene-1,3-dihydroimidazol-4-yl)propan-2-yl]azanium C9 H16 N3 O2 S SSISHJJTAXXQAX-ZETCQYMHSA-O
EDO	I [auth A], N [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	F [auth A], G [auth A], H [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], D [auth A], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A, B	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS
TSY	A, B	L-PEPTIDE LINKING	C3 H7 N O2 S3		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.214 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.72	α = 90
b = 88	β = 90.46
c = 90.57	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Wu, L., Liu, P.H., Zhou, J.H.

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description