6YXZ | pdb_00006yxz

Structure and activity of the GH20 beta-N-beta-N-acetylhexosaminidase from Bifidobacterium bifidum

• PDB DOI: https://doi.org/10.2210/pdb6YXZ/pdb

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


• Deposited: 2020-05-04 Released: 2021-05-12 
• Deposition Author(s): He, Y., Jin, Y.
• Funding Organization(s): Wellcome Trust, National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.220 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.170 (DCC) 

Starting Model: other

Literature

Structure and activity of the GH20 beta-N-beta-N-acetylhexosaminidase from Bifidobacterium bifidum

He, Y., Jin, Y.

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: 108.72 kDa 
• Atom Count: 5,955 
• Modeled Residue Count: 698 
• Deposited Residue Count: 1,010 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-N-acetylhexosaminidase	A [auth JJJ]	1,010	Bifidobacterium bifidum	Mutation(s): 0  Gene Names: bbhII, B0085_1802, LMG11583_1629 EC: 3.2.1.52
UniProt
Find proteins for D4QAP5 (Bifidobacterium bifidum) Explore D4QAP5  Go to UniProtKB:  D4QAP5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth JJJ]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	F [auth JJJ]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	E [auth JJJ]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth JJJ], D [auth JJJ]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.220 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.170 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.566	α = 90
b = 126.75	β = 90
c = 152.71	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
SHELXDE	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-05-12 
Deposition Author(s): He, Y., Jin, Y.

---

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	209057/Z/ 17/Z
National Natural Science Foundation of China (NSFC)	China	31400663

Revision History  

• Version 1.0: 2021-05-12
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary