5MGC

STRUCTURE OF E298Q-BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER IN COMPLEX WITH 4-Galactosyl-lactose

• PDB DOI: https://doi.org/10.2210/pdb5MGC/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus niger CBS 513.88
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2016-11-21 Released: 2017-04-19 
• Deposition Author(s): Rico-Diaz, A., Ramirez-Escudero, M., Vizoso Vazquez, A., Cerdan, M.E., Becerra, M., Sanz-Aparicio, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.204 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

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: 116.65 kDa 
• Atom Count: 8,083 
• Modelled Residue Count: 968 
• Deposited Residue Count: 1,013 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable beta-galactosidase A	A	1,013	Aspergillus niger CBS 513.88	Mutation(s): 1  Gene Names: lacA, An01g12150 EC: 3.2.1.23
UniProt
Find proteins for A2QAN3 (Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513)) Explore A2QAN3  Go to UniProtKB:  A2QAN3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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	B	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G83582BK GlyCosmos:  G83582BK GlyGen:  G83582BK

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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	10		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G40702WU GlyCosmos:  G40702WU GlyGen:  G40702WU

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G01760ZU GlyCosmos:  G01760ZU GlyGen:  G01760ZU

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	E	3		N/A
Glycosylation Resources
GlyTouCan:  G33559CW GlyCosmos:  G33559CW GlyGen:  G33559CW

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.204 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.627	α = 90
b = 106.659	β = 96.13
c = 84.425	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): Rico-Diaz, A., Ramirez-Escudero, M., Vizoso Vazquez, A., Cerdan, M.E., Becerra, M., Sanz-Aparicio, J.

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2017-06-28
  Changes: Database references
• 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, Derived calculations, Refinement description, Structure summary