5Z1B

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycosyl hydrolase family 2, TIM barrel domain proteinA, B, C, D692Bifidobacterium dentium ATCC 27679Mutation(s): 1 
Gene Names: uidAHMPREF0168_2111
EC: 3.2.1.31
UniProt
Find proteins for E0QAF3 (Bifidobacterium dentium ATCC 27679)
Explore E0QAF3 
Go to UniProtKB:  E0QAF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0QAF3
Protein Feature View
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  • Reference Sequence
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 = 91.34α = 90
b = 104.165β = 90.4
c = 160.673γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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