8STB

The structure of abxF, an enzyme catalyzing the formation of the chiral spiroketal of an anthrabenzoxocinone antibiotic, (-)-ABX

• PDB DOI: https://doi.org/10.2210/pdb8STB/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces sp.
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-05-09 Released: 2024-05-22 
• Deposition Author(s): Luo, Z., Jia, X., Yan, X., Qu, X., Kobe, B.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.234 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

Starting Model: experimental

Literature

The crystal structure of abxF, an enzyme catalyzing the formation of the chiral spiroketal of an anthrabenzoxocinone antibiotic, (-)-ABX.

Luo, Z., Jia, X., Yan, X., Qu, X., Kobe, B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: NMR Distance Restraints, gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.35 kDa 
• Atom Count: 3,263 
• Modelled Residue Count: 432 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase	A [auth B], B [auth A]	234	Streptomyces sp.	Mutation(s): 0  Gene Names: abxF
UniProt
Find proteins for A0A2I6B3F9 (Streptomyces sp) Explore A0A2I6B3F9  Go to UniProtKB:  A0A2I6B3F9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.234 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.029	α = 90
b = 76.029	β = 90
c = 166.752	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Luo, Z., Jia, X., Yan, X., Qu, X., Kobe, B.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	FL180100109

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release