6Z14

Structure of Bifidobacterium bifidum GH20 beta-N-beta-N-acetylhexosaminidase E553Q variant in complex with 4MU-6SGlcNAc-derived oxazoline

• PDB DOI: https://doi.org/10.2210/pdb6Z14/pdb

• Classification: HYDROLASE
• Organism(s): Bifidobacterium bifidum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-05-12 Released: 2021-05-19 
• Deposition Author(s): He, Y., Jin, Y., Rizkallah, P., Chen, P.
• Funding Organization(s): Wellcome Trust, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.205 
• R-Value Work: 0.160 

Starting Model: experimental

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: 109.16 kDa 
• Atom Count: 5,979 
• Modelled Residue Count: 694 
• 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): 1  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
Q4Z (Subject of Investigation/LOI)	D [auth JJJ]	[(3~{a}~{R},5~{R},6~{S},7~{R},7~{a}~{R})-2-methyl-6,7-bis(oxidanyl)-5,6,7,7~{a}-tetrahydro-3~{a}~{H}-pyrano[3,2-d][1,3]oxazol-1-ium-5-yl]methyl sulfate C8 H13 N O8 S JTXHTZSXIURMTP-PVFLNQBWSA-N
B3P	C [auth JJJ]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N
NO3	B [auth JJJ]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
NA	E [auth JJJ], F [auth JJJ]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.205 
• R-Value Work: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.423	α = 90
b = 124.884	β = 90
c = 151.682	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-05-19 
Deposition Author(s): He, Y., Jin, Y., Rizkallah, P., Chen, P.

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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: 2021-05-19
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description