7EQK | pdb_00007eqk

Structural and mechanistic studies of a novel non-heme iron epimerase/lyase and its utilization in chemoselective synthesis.

• PDB DOI: https://doi.org/10.2210/pdb7EQK/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces albus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-05-03 Released: 2022-03-16 
• Deposition Author(s): Li, T.L., Li, Y.S., Chen, M.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Structural and Mechanistic Bases for StnK3 and Its Mutant-Mediated Lewis-Acid-Dependent Epimerization and Retro-Aldol Reactions.

Chen, M.H., Li, Y.S., Hsu, N.S., Lin, K.H., Wang, Y.L., Wang, Z.C., Chang, C.F., Lin, J.P., Chang, C.Y., Li, T.L.

(2022) ACS Catal 12: 1945-1956

• DOI: https://doi.org/10.1021/acscatal.1c04790

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

Macromolecule Content 

• Total Structure Weight: 28.23 kDa 
• Atom Count: 1,899 
• Modeled Residue Count: 237 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin domain-containing protein	A, B	131	Streptomyces albus	Mutation(s): 0  Gene Names: stnK3, G3260_000576
UniProt
Find proteins for L7PIL3 (Streptomyces albus) Explore L7PIL3  Go to UniProtKB:  L7PIL3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JAX (Subject of Investigation/LOI)	G [auth B]	(E)-3-(1H-indol-3-yl)-2-oxidanyl-but-2-enoic acid C12 H11 N O3 PPGRYTGRWGDNAP-YRNVUSSQSA-N
5RN (Subject of Investigation/LOI)	E [auth A]	1-(1~{H}-indol-3-yl)ethanone C10 H9 N O VUIMBZIZZFSQEE-UHFFFAOYSA-N
GOA (Subject of Investigation/LOI)	D [auth A]	GLYCOLIC ACID C2 H4 O3 AEMRFAOFKBGASW-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)	C [auth A], F [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.782	α = 90
b = 66.782	β = 90
c = 116.336	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-03-16 
Deposition Author(s): Li, T.L., Li, Y.S., Chen, M.H.

Revision History  

• Version 1.0: 2022-03-16
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations, Refinement description
• Version 2.1: 2023-11-29
  Changes: Refinement description