5LWX | pdb_00005lwx

Crystal structure of the H253D mutant of McoG from Aspergillus niger

• PDB DOI: https://doi.org/10.2210/pdb5LWX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus niger
• Expression System: Aspergillus niger
• Mutation(s): Yes 


• Deposited: 2016-09-19 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: 1.49 Å
• R-Value Free: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

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: 67.75 kDa 
• Atom Count: 5,174 
• Modeled Residue Count: 554 
• Deposited Residue Count: 577 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multicopper oxidase	A	577	Aspergillus niger	Mutation(s): 1  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: 1

Oligosaccharides

Help  

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth A], J [auth A], K [auth A], M [auth A], N [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA	I [auth A], O [auth A]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
MAN	L [auth A], P [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
CU	D [auth A], E [auth A], F [auth A], G [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
PER	Q [auth A]	PEROXIDE ION O2 ANAIPYUSIMHBEL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.273	α = 90
b = 60.498	β = 94.96
c = 53.744	γ = 90

Software Package:

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

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: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary