9J1X | pdb_00009j1x

Structure of mutant evolved from PaDa-I, unspecific peroxygenase from Agrocybe aegerita

• PDB DOI: https://doi.org/10.2210/pdb9J1X/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Cyclocybe aegerita
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2024-08-06 Released: 2025-08-13 
• Deposition Author(s): Liu, W., Zhang, J., Zhang, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: in silico

Literature

Structure of mutant evolved from PaDa-I, unspecific peroxygenase from Agrocybe aegerita

Liu, W., Zhang, J., Zhang, W.

To be published.

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

Macromolecule Content 

• Total Structure Weight: 36.95 kDa 
• Atom Count: 2,911 
• Modeled Residue Count: 325 
• Deposited Residue Count: 325 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic peroxygenase	A	325	Cyclocybe aegerita	Mutation(s): 0  Gene Names: APO1 EC: 1.11.2.1
UniProt
Find proteins for B9W4V6 (Cyclocybe aegerita) Explore B9W4V6  Go to UniProtKB:  B9W4V6
Glycosylation
Glycosylation Sites: 3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	F [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NAG (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG (Subject of Investigation/LOI)	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.091	α = 90
b = 57.907	β = 110.34
c = 60.699	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Liu, W., Zhang, J., Zhang, W.

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

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release