8U2A

Crystal structure of NanI in complex with Neu5,9Ac

• PDB DOI: https://doi.org/10.2210/pdb8U2A/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium perfringens ATCC 13124
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-09-05 Released: 2024-09-04 
• Deposition Author(s): Medley, B.J., Boraston, A.B.
• Funding Organization(s): Canadian Glycomics Network (GLYCONET)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.250 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Starting Model: experimental

Literature

A terminal case of glycan catabolism: structural and enzymatic characterization of the sialidases of Clostridium perfringens

Medley, B.J., Low, K.E., Garber, J.M., Gray, T.E., Liu, L., Klassen, L., Fordwour, O.B., Inglis, G.D., Boons, G.J., Zandberg, W.F., Abbott, W., Boraston, A.B.

To be published.

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: 50.58 kDa 
• Atom Count: 3,692 
• Modelled Residue Count: 448 
• Deposited Residue Count: 448 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exo-alpha-sialidase	A	448	Clostridium perfringens ATCC 13124	Mutation(s): 0  Gene Names: nanI

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5N6 (Subject of Investigation/LOI)	F [auth A]	9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid C13 H21 N O10 NYWZBRWKDRMPAS-CTAKWSDESA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	B [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.250 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.482	α = 90
b = 72.331	β = 90
c = 97.347	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Medley, B.J., Boraston, A.B.

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Funding Organization	Location	Grant Number
Canadian Glycomics Network (GLYCONET)	Canada	--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release