5G0M | pdb_00005g0m

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.213 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

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.

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)

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J13	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
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.213 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	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

Entry History 

Deposition Data

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

Revision History  

• 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