8K2K

Crystal structure of Group 3 Oligosaccharide/Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaDssm in complex with GalNAc-thiazoline

• PDB DOI: https://doi.org/10.2210/pdb8K2K/pdb

• Classification: HYDROLASE
• Organism(s): metagenome
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-12 Released: 2024-04-24 
• Deposition Author(s): Sumida, T., Fushinobu, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Mizutani Foundation for Glycoscience

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.206 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Literature

Genetic and functional diversity of beta-N-acetylgalactosamine residue-targeting glycosidases expanded by deep-sea metagenome

Sumida, T., Hiraoka, S., Usui, K., Ishiwata, A., Sengoku, T., Stubbs, K.A., Tanaka, K., Deguchi, S., Fushinobu, S., Nunoura, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 62.8 kDa 
• Atom Count: 4,739 
• Modelled Residue Count: 529 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligosaccharide/Monosaccharide-releasing beta-N-acetylgalactosaminidase	A	542	metagenome	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNL	B [auth A]	(3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol C8 H13 N O4 S DRHXTSWSUAJOJZ-JAJWTYFOSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.206 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.537	α = 90
b = 53.537	β = 90
c = 428.292	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Sumida, T., Fushinobu, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP22K05398
Japan Society for the Promotion of Science (JSPS)	Japan	JP20K15444
Mizutani Foundation for Glycoscience	Japan	FT100100291

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release