5G0M

beta-glucuronidase with an activity-based probe (N-acyl cyclophellitol aziridine) bound

PDB DOI: https://doi.org/10.2210/pdb5G0M/pdb

Classification: HYDROLASE
Organism(s): Acidobacterium capsulatum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-03-21 Released: 2017-04-12
Deposition Author(s): Jin, Y., Wu, L., Jiang, J.B., Overkleeft, H.S., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 ?
R-Value Free: 0.213
R-Value Work: 0.183
R-Value Observed: 0.184

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The Structure of a Bacteria Beta-Glucuronidase in Gh79 Family

Jin, Y., Wu, L., Jiang, J.B., Overkleeft, H.S., Davies, G.J.

To be published.

Macromolecule Content

Total Structure Weight: 51.38 kDa
Atom Count: 3,719
Modelled Residue Count: 457
Deposited Residue Count: 475
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-GLUCURONIDASE	A	475	Acidobacterium capsulatum	Mutation(s): 0 EC: 3.2.1.31
UniProt
Find proteins for C1F2K5 (Acidobacterium capsulatum (strain ATCC 51196 / DSM 11244 / BCRC 80197 / JCM 7670 / NBRC 15755 / NCIMB 13165 / 161)) Explore C1F2K5 Go to UniProtKB: C1F2K5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C1F2K5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J13 Query on J13 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(1S,2R,3R,4S,6S)-6-[(8-azidooctanoyl)amino]-2,3,4-trihydroxycyclohexane-1-carboxylate C₁₅ H₂₆ N₄ O₇ BTDXZNFDEBZDRR-KTEZLCCFSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 ?
R-Value Free: 0.213
R-Value Work: 0.183
R-Value Observed: 0.184
Space Group: C 1 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 150.74	α = 90
b = 44.81	β = 115.5
c = 83.27	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-04-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-04-12
Type: Initial release
Version 1.1: 2019-05-22
Changes: Data collection, Derived calculations, Experimental preparation
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary

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Help and Resources

5G0M

beta-glucuronidase with an activity-based probe (N-acyl cyclophellitol aziridine) bound

The Structure of a Bacteria Beta-Glucuronidase in Gh79 Family

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)