5Z1B | pdb_00005z1b

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.160 (Depositor), 0.162 (DCC)
R-Value Work:
0.130 (Depositor), 0.136 (DCC)
R-Value Observed:
0.130 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 309.95 kDa
Atom Count: 22,105
Modeled Residue Count: 2,493
Deposited Residue Count: 2,768
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E0QAF3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BDP Query on BDP Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	beta-D-glucopyranuronic acid C₆ H₁₀ O₇ AEMOLEFTQBMNLQ-QIUUJYRFSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
SE2 Query on SE2 Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	3-HYDROXY-2H-CHROMEN-2-ONE C₉ H₆ O₃ MJKVTPMWOKAVMS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.160 (Depositor), 0.162 (DCC)
R-Value Work: 0.130 (Depositor), 0.136 (DCC)
R-Value Observed: 0.130 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-12-12

Deposition Author(s):

Dashnyam, P.

Lin, H.Y.

Lin, C.H.

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
Version 1.2: 2024-03-27
Changes: Data collection, Database references, Refinement description, Structure summary

5Z1B | pdb_00005z1b

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

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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