5Z19 | pdb_00005z19

The crystal structure of Ruminococcus gnavus beta-glucuronidase in complex with uronic isofagomine

• PDB DOI: https://doi.org/10.2210/pdb5Z19/pdb

• Classification: HYDROLASE
• Organism(s): Mediterraneibacter gnavus
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 2.50 Å
• R-Value Free: 
  0.209 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Dissection of the substrate preference and structure of gut microbial beta-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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 437.58 kDa 
• Atom Count: 29,830 
• Modeled Residue Count: 3,587 
• Deposited Residue Count: 3,762 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucuronidase	A, B, C, D, E, F	627	Mediterraneibacter gnavus	Mutation(s): 0  Gene Names: uidA EC: 3.2.1.31
UniProt
Find proteins for Q6W7J7 (Mediterraneibacter gnavus) Explore Q6W7J7  Go to UniProtKB:  Q6W7J7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SJ5	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	(3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid C6 H11 N O4 SSMLJUWXZFXWSF-VPENINKCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.209 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.282	α = 90
b = 112.359	β = 93.45
c = 209.795	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
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: 2019-04-03
  Changes: Data collection, Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references, Refinement description