7CBO | pdb_00007cbo

Crystal structure of beta-N-acetylhexosaminidase Am0868 from Akkermansia muciniphila in complex with GlcNAc

• PDB DOI: https://doi.org/10.2210/pdb7CBO/pdb

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


• Deposited: 2020-06-13 Released: 2020-08-12 
• Deposition Author(s): Xu, W., Wang, M., Zhang, M.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Structural and biochemical analyses of beta-N-acetylhexosaminidase Am0868 from Akkermansia muciniphila involved in mucin degradation.

Xu, W., Yang, W., Wang, Y., Wang, M., Zhang, M.

(2020) Biochem Biophys Res Commun 529: 876-881

• DOI: https://doi.org/10.1016/j.bbrc.2020.06.116

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: 61.54 kDa 
• Atom Count: 5,044 
• Modeled Residue Count: 522 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-N-acetylhexosaminidase	A	538	Akkermansia muciniphila ATCC BAA-835	Mutation(s): 0  Gene Names: Amuc_0868 EC: 3.2.1.52
UniProt
Find proteins for B2UQG6 (Akkermansia muciniphila (strain ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc)) Explore B2UQG6  Go to UniProtKB:  B2UQG6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.231	α = 90
b = 72.132	β = 90
c = 138.228	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Xu, W., Wang, M., Zhang, M.

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Funding Organization	Location	Grant Number
Other government	China	KJ2019ZD02

Revision History  

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description