6TBQ

AA13 Lytic polysaccharide monooxygenase from Aspergillus oryzae partially in Cu(II) state

• PDB DOI: https://doi.org/10.2210/pdb6TBQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus oryzae RIB40
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2019-11-04 Released: 2020-03-18 
• Deposition Author(s): Muderspach, S.J., Lo Leggio, L., Tandrup, T., Frandsen, K.E.H., Poulsen, J.C.N.
• Funding Organization(s): Novo Nordisk Foundation, Danish Council for Independent Research, European Communitys Seventh Framework Programme

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.263 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 

Literature

Further structural studies of the lytic polysaccharide monooxygenase AoAA13 belonging to the starch-active AA13 family

Muderspach, S.J., Tandrup, T., Frandsen, K.E.H., Santoni, G., Poulsen, J.C.N., Lo Leggio, L.

(2019) Amylase 3(1): 41-54

• DOI: https://doi.org/10.1515/amylase-2019-0004

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.3 kDa 
• Atom Count: 1,995 
• Modelled Residue Count: 233 
• Deposited Residue Count: 233 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AoAA13	A	233	Aspergillus oryzae RIB40	Mutation(s): 0  Gene Names: AO090701000246
UniProt
Find proteins for Q2U8Y3 (Aspergillus oryzae (strain ATCC 42149 / RIB 40)) Explore Q2U8Y3  Go to UniProtKB:  Q2U8Y3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC	A	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.263 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.305	α = 90
b = 61.316	β = 90
c = 72.982	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Muderspach, S.J., Lo Leggio, L., Tandrup, T., Frandsen, K.E.H., Poulsen, J.C.N.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF17SA0027704
Danish Council for Independent Research	Denmark	8021-00273B
European Communitys Seventh Framework Programme	Denmark	N283570

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary