8URL

The Apo NanJ structure from Clostridium perfringens

• PDB DOI: https://doi.org/10.2210/pdb8URL/pdb

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


• Deposited: 2023-10-26 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: 2.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Starting Model: experimental

Literature

The apo structure of NanJ from 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, D.W.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 50.13 kDa 
• Atom Count: 3,467 
• Modelled Residue Count: 446 
• Deposited Residue Count: 449 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exo-alpha-sialidase NanJ	A	449	Clostridium perfringens	Mutation(s): 0  Gene Names: nanJ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.226	α = 90
b = 48.804	β = 93.948
c = 73.324	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