8AV5

Glycosylated PaDa-I mutant of Unspecific Peroxygenase from Agrocybe aegerita

• PDB DOI: https://doi.org/10.2210/pdb8AV5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cyclocybe aegerita
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2022-08-26 Released: 2023-08-02 
• Deposition Author(s): Mielke, T.F., Grogan, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.210 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Glycosylated PaDa-I mutant of Unspecific Peroxygenase from Agrocybe aegerita

Mielke, T.F., Grogan, G.

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: 39.08 kDa 
• Atom Count: 3,105 
• Modelled Residue Count: 324 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic peroxygenase	A	324	Cyclocybe aegerita	Mutation(s): 5  Gene Names: APO1 EC: 1.11.2.1
UniProt
Find proteins for B9W4V6 (Cyclocybe aegerita) Explore B9W4V6  Go to UniProtKB:  B9W4V6
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G55143WF GlyCosmos:  G55143WF GlyGen:  G55143WF

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	H [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NAG	G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ACT	I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.210 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.66	α = 90
b = 77.66	β = 90
c = 123.883	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-02 
Deposition Author(s): Mielke, T.F., Grogan, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-08-02
  Type: Initial release