5LM8

Crystal structure of a laccase-like multicopper oxidase McoG from from Aspergillus niger

• PDB DOI: https://doi.org/10.2210/pdb5LM8/pdb

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


• Deposited: 2016-07-29 Released: 2017-05-03 
• Deposition Author(s): Ferraroni, M., Briganti, F., Tamayo-Ramos, J.A., van Berkel, W.J.H., Westphal, A.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.222 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Starting Model: experimental

Literature

Structure and function of Aspergillus niger laccase McoG

Ferraroni, M., Westphal, A.H., Borsari, M., Tamayo-Ramos, J.A., Briganti, F., de Graaff, L.H., van Berkel, W.J.H.

(2017) Biocatalysis 

• DOI: https://doi.org/10.1515/boca-2017-0001

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.63 kDa 
• Atom Count: 5,160 
• Modelled Residue Count: 549 
• Deposited Residue Count: 549 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
'Multicopper oxidase	A	549	Aspergillus niger	Mutation(s): 0  Gene Names: An08g08450 EC: 1.10.3.2
UniProt
Find proteins for A2QS62 (Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513)) Explore A2QS62  Go to UniProtKB:  A2QS62
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[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	C	5		N/A
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N/A
Glycosylation Resources
GlyTouCan:  G90333CG GlyCosmos:  G90333CG GlyGen:  G90333CG

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A], K [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CU	F [auth A], G [auth A], H [auth A], I [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
PER	L [auth A]	PEROXIDE ION O2 ANAIPYUSIMHBEL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.222 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.709	α = 90
b = 61.346	β = 95.29
c = 53.836	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Ferraroni, M., Briganti, F., Tamayo-Ramos, J.A., van Berkel, W.J.H., Westphal, A.H.

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2017-05-17
  Changes: Database references
• Version 1.2: 2017-07-19
  Changes: Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary