8UVV

The NanJ sialidase catalytic domain in complex with Neu5Ac

PDB DOI: https://doi.org/10.2210/pdb8UVV/pdb

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

Deposited: 2023-11-04 Released: 2024-09-04
Deposition Author(s): Medley, B.J., Boraston, A.B.
Funding Organization(s): Canadian Glycomics Network (GLYCONET)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.253
R-Value Work: 0.217
R-Value Observed: 0.219

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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, D.W.

To be published.

Macromolecule Content

Total Structure Weight: 50.43 kDa
Atom Count: 3,620
Modelled Residue Count: 449
Deposited Residue Count: 449
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exo-alpha-sialidase NanJ	A	449	Clostridium perfringens	Mutation(s): 0 Gene Names: nanJ
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA (Subject of Investigation/LOI) Query on SIA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain D [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.253
R-Value Work: 0.217
R-Value Observed: 0.219
Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.134	α = 90
b = 171.134	β = 90
c = 92.843	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.