6YDD

X-ray structure of LPMO.

• PDB DOI: https://doi.org/10.2210/pdb6YDD/pdb

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


• Deposited: 2020-03-20 Released: 2020-09-16 
• Deposition Author(s): Tandrup, T., Tryfona, T., Frandsen, K.E.H., Johansen, K.S., Dupree, P., Lo Leggio, L.
• Funding Organization(s): Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.261 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 56.72 kDa 
• Atom Count: 3,656 
• Modelled Residue Count: 448 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LPMO lytic polysaccharide monooxygenase	A, B	252	Achaetomiella virescens	Mutation(s): 0  Gene Names: aa9
UniProt
Find proteins for A0A223GEC9 (Collariella virescens) Explore A0A223GEC9  Go to UniProtKB:  A0A223GEC9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C	4		N/A
Glycosylation Resources
GlyTouCan:  G00025MO GlyCosmos:  G00025MO GlyGen:  G00025MO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	D	2		N/A
Glycosylation Resources
GlyTouCan:  G84824ZO GlyCosmos:  G84824ZO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU (Subject of Investigation/LOI)	E [auth A], F [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

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

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900011	C	beta-cellotetraose	Oligosaccharide / Metabolism

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005	D	beta-cellobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.261 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.14	α = 90
b = 39.7	β = 93.49
c = 120.65	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Tandrup, T., Tryfona, T., Frandsen, K.E.H., Johansen, K.S., Dupree, P., Lo Leggio, L.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF17SA0027704

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Database references
• Version 2.0: 2022-04-20
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-03-08
  Changes: Structure summary
• Version 2.2: 2024-02-07
  Changes: Data collection, Refinement description