2BF6

Atomic Resolution Structure of the bacterial sialidase NanI from Clostridium perfringens in complex with alpha-Sialic Acid (Neu5Ac).

• PDB DOI: https://doi.org/10.2210/pdb2BF6/pdb

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


• Deposited: 2004-12-04 Released: 2006-03-09 
• Deposition Author(s): Newstead, S., Taylor, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free: 0.133 
• R-Value Observed: 0.113 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 50.67 kDa 
• Atom Count: 4,089 
• Modelled Residue Count: 449 
• Deposited Residue Count: 449 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EXO-ALPHA-SIALIDASE	A	449	Clostridium perfringens	Mutation(s): 0  EC: 3.2.1.18
UniProt
Find proteins for Q59310 (Clostridium perfringens) Explore Q59310  Go to UniProtKB:  Q59310

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA	B [auth A]	N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free: 0.133 
• R-Value Observed: 0.113 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.981	α = 90
b = 69.413	β = 90
c = 72.694	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-09 
Deposition Author(s): Newstead, S., Taylor, G.L.

Revision History  

• Version 1.0: 2006-03-09
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-07
  Changes: Advisory, Source and taxonomy
• Version 1.4: 2019-05-22
  Changes: Data collection, Refinement description
• Version 1.5: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.6: 2023-12-13
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary