5Z1A | pdb_00005z1a

The crystal structure of Bacteroides fragilis beta-glucuronidase in complex with uronic isofagomine

PDB DOI: https://doi.org/10.2210/pdb5Z1A/pdb

Classification: HYDROLASE
Organism(s): Bacteroides fragilis NCTC 9343
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: 1.86 Å
R-Value Free:
0.190 (Depositor), 0.186 (DCC)
R-Value Work:
0.153 (Depositor)
R-Value Observed:
0.154 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5Z1A

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.

Macromolecule Content

Total Structure Weight: 78.05 kDa
Atom Count: 6,167
Modeled Residue Count: 655
Deposited Residue Count: 680
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative beta-galactosidase	A	680	Bacteroides fragilis NCTC 9343	Mutation(s): 0 Gene Names: BF9343_0320 EC: 3.2.1.31
UniProt
Find proteins for Q5LIC7 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LIC7 Go to UniProtKB: Q5LIC7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5LIC7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SJ5 (Subject of Investigation/LOI) Query on SJ5 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid C₆ H₁₁ N O₄ SSMLJUWXZFXWSF-VPENINKCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.190 (Depositor), 0.186 (DCC)
R-Value Work: 0.153 (Depositor)
R-Value Observed: 0.154 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.253	α = 90
b = 103.135	β = 90
c = 199.147	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

Ligand Structure Quality Assessment

View more in-depth experimental data

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.