8HLS

Crystal structure of the sialidase Am1547 from A.muciniphila

• PDB DOI: https://doi.org/10.2210/pdb8HLS/pdb

• Classification: HYDROLASE
• Organism(s): Akkermansia muciniphila ATCC BAA-835
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2022-11-30 Released: 2024-06-05 
• Deposition Author(s): Rui, B., Xinyue, T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.223 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

Structural analysis of a novel sialidase from Akkermansia muciniphila reveals a distinct catalytic motif in GH33 family

Xinyue, T., Rui, B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 134.81 kDa 
• Atom Count: 9,210 
• Modelled Residue Count: 1,144 
• Deposited Residue Count: 1,202 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialidase domain-containing protein	A, B	601	Akkermansia muciniphila ATCC BAA-835	Mutation(s): 0  Gene Names: Amuc_1547
UniProt
Find proteins for B2ULI1 (Akkermansia muciniphila (strain ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc)) Explore B2ULI1  Go to UniProtKB:  B2ULI1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.223 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.16	α = 90
b = 56.771	β = 94.01
c = 145.932	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Rui, B., Xinyue, T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81871615

Revision History  

• Version 1.0: 2024-06-05
  Type: Initial release