8YXS | pdb_00008yxs

X-ray structure of non-heme iron dioxygenase from Aspergillus brunneoviolaceus

• PDB DOI: https://doi.org/10.2210/pdb8YXS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus brunneoviolaceus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-04-02 Released: 2025-04-09 
• Deposition Author(s): Lv, X., Ma, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.62 Å
• R-Value Free: 
  0.312 (Depositor), 0.308 (DCC) 
• R-Value Work: 
  0.276 (Depositor), 0.278 (DCC) 
• R-Value Observed: 
  0.278 (Depositor) 

Starting Model: experimental

Literature

Switching Regioselectivity in the Enzymatic Fission of Anthraquinones

Lv, X., Ma, X.

To be published.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 256.72 kDa 
• Atom Count: 17,736 
• Modeled Residue Count: 2,230 
• Deposited Residue Count: 2,280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase AflY	A, B, C, D, E	456	Aspergillus brunneoviolaceus	Mutation(s): 1  Gene Names: BO72DRAFT_450687
UniProt
Find proteins for A0A1L9WLE0 (Aspergillus aculeatus (strain ATCC 16872 / CBS 172.66 / WB 5094)) Explore A0A1L9WLE0  Go to UniProtKB:  A0A1L9WLE0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	F [auth A], G [auth B], H [auth C], I [auth D], J [auth E]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B, C, D, E	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.62 Å
• R-Value Free:  0.312 (Depositor), 0.308 (DCC) 
• R-Value Work:  0.276 (Depositor), 0.278 (DCC) 
• R-Value Observed: 0.278 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 256.987	α = 90
b = 109.736	β = 93.39
c = 179.891	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Lv, X., Ma, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81991524

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release