5Z18

The crystal structure of Ruminococcus gnavus beta-glucuronidase

PDB DOI: https://doi.org/10.2210/pdb5Z18/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.209
R-Value Work: 0.167
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 436.61 kDa
Atom Count: 30,433
Modelled Residue Count: 3,519
Deposited Residue Count: 3,762
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucuronidase	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6W7J7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.209
R-Value Work: 0.167
R-Value Observed: 0.168
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.868	α = 90
b = 118.182	β = 93.45
c = 210.355	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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-12-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-12-12
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.