6TC4 | pdb_00006tc4

AA13 Lytic polysaccharide monooxygenase from Aspergillus oryzae measured with SSX

• PDB DOI: https://doi.org/10.2210/pdb6TC4/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Aspergillus oryzae RIB40
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2019-11-05 Released: 2020-03-18 
• Deposition Author(s): Tandrup, T., Muderspach, S.J., Frandsen, K.E.H., Santoni, G., Poulsen, J.C.N., Lo Leggio, L.
• 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: 2.00 Å
• R-Value Free: 
  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.93 kDa 
• Atom Count: 2,020 
• 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
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4	P [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 2.00 Å
• R-Value Free:  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.72	α = 90
b = 61.43	β = 90
c = 73.78	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): Tandrup, T., Muderspach, S.J., Frandsen, K.E.H., Santoni, G., Poulsen, J.C.N., Lo Leggio, L.

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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