5Z1B

Structure of Bifidobacterium dentium beta-glucuronidase complexed with coumarin-3-O-glucuronide

• PDB DOI: https://doi.org/10.2210/pdb5Z1B/pdb

• Classification: HYDROLASE
• Organism(s): Bifidobacterium dentium ATCC 27679
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-12-25 Released: 2018-12-12 
• Deposition Author(s): Dashnyam, P., Lin, H.Y., Lin, C.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.160 
• R-Value Work: 0.130 
• R-Value Observed: 0.130 

Literature

Dissection of the substrate preference and structure of gut microbial-glucuronidases identifies the major bacteria causing xenobiotic toxicity

Dashnyam, P., Mudududdla, R., Hsieh, T.J., Lin, T.C., Lin, H.Y., Chen, P.Y., Hsu, C.Y., Lin, C.H.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 309.95 kDa 
• Atom Count: 22,105 
• Modelled Residue Count: 2,493 
• Deposited Residue Count: 2,768 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 2, TIM barrel domain protein	A, B, C, D	692	Bifidobacterium dentium ATCC 27679	Mutation(s): 1  Gene Names: uidA, HMPREF0168_2111 EC: 3.2.1.31
UniProt
Find proteins for E0QAF3 (Bifidobacterium dentium ATCC 27679) Explore E0QAF3  Go to UniProtKB:  E0QAF3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BDP	E [auth A], G [auth B], I [auth C], K [auth D]	beta-D-glucopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-QIUUJYRFSA-N
SE2	F [auth A], H [auth B], J [auth C], L [auth D]	3-HYDROXY-2H-CHROMEN-2-ONE C9 H6 O3 MJKVTPMWOKAVMS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.160 
• R-Value Work: 0.130 
• R-Value Observed: 0.130 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.34	α = 90
b = 104.165	β = 90.4
c = 160.673	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Dashnyam, P., Lin, H.Y., Lin, C.H.

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references, Refinement description, Structure summary