3WY3

Crystal structure of alpha-glucosidase mutant D202N in complex with glucose and glycerol

• PDB DOI: https://doi.org/10.2210/pdb3WY3/pdb

• Classification: HYDROLASE
• Organism(s): Halomonas sp. H11
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-08-18 Released: 2015-06-10 
• Deposition Author(s): Shen, X., Gai, Z., Kato, K., Yao, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.244 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

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: 123.13 kDa 
• Atom Count: 8,634 
• Modelled Residue Count: 1,070 
• Deposited Residue Count: 1,076 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-glucosidase	A, B	538	Halomonas sp. H11	Mutation(s): 1  Gene Names: aglA EC: 3.2.1.20
UniProt
Find proteins for H3K096 (Halomonas sp. H11) Explore H3K096  Go to UniProtKB:  H3K096

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	F [auth A], J [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
GOL	D [auth A], E [auth A], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.244 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.53	α = 90
b = 119.57	β = 90
c = 177.94	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-10 
Deposition Author(s): Shen, X., Gai, Z., Kato, K., Yao, M.

Revision History  

• Version 1.0: 2015-06-10
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2018-03-21
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2024-03-20
  Changes: Data collection, Database references, Refinement description, Structure summary