6KTV

The structure of EanB complex with hercynine and persulfided Cys412

• PDB DOI: https://doi.org/10.2210/pdb6KTV/pdb

• Classification: TRANSFERASE
• Organism(s): Chlorobium limicola
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2019-08-29 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: 2.20 Å
• R-Value Free: 0.199 
• 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.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 54.53 kDa 
• Atom Count: 3,830 
• Modelled Residue Count: 431 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfurtransferase	A	460	Chlorobium limicola	Mutation(s): 0  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 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AVJ (Subject of Investigation/LOI)	B [auth A]	N,N,N-trimethyl-histidine C9 H16 N3 O2 GPPYTCRVKHULJH-QMMMGPOBSA-O
PG4	AA [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	Z [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	L [auth A], M [auth A], N [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
PDO	BA [auth A], CA [auth A], DA [auth A]	1,3-PROPANDIOL C3 H8 O2 YPFDHNVEDLHUCE-UHFFFAOYSA-N
IMD	EA [auth A], FA [auth A], GA [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO	O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	HA [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.199 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.675	α = 90
b = 112.819	β = 90
c = 60.615	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	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