7PSJ

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor VL166

• PDB DOI: https://doi.org/10.2210/pdb7PSJ/pdb

• Classification: CARBOHYDRATE
• Organism(s): Acidobacterium capsulatum ATCC 51196
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-09-23 Released: 2022-08-03 
• Deposition Author(s): Armstrong, Z., Wu, L., Davies, G.J.
• Funding Organization(s): European Research Council (ERC), Netherlands Organisation for Scientific Research (NWO), Israel Science Foundation, European Molecular Biology Organization (EMBO), Royal Society, Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.223 
• R-Value Work: 0.195 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.23 kDa 
• Atom Count: 3,718 
• Modelled Residue Count: 435 
• 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 ATCC 51196	Mutation(s): 0  Gene Names: ACP_2665
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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-(2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexane-1-carboxylic acid	B	2	N/A	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.223 
• R-Value Work: 0.195 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.393	α = 90
b = 44.117	β = 97.579
c = 136.708	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-03 
Deposition Author(s): Armstrong, Z., Wu, L., Davies, G.J.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	United Kingdom	ERC-2011-AdG-290836
European Research Council (ERC)	United Kingdom	ERC-2012-AdG-322942
Netherlands Organisation for Scientific Research (NWO)	United Kingdom	--
Israel Science Foundation	United Kingdom	1021/19
European Molecular Biology Organization (EMBO)	United Kingdom	STF8184
Royal Society	United Kingdom	--
Wellcome Trust	United Kingdom	218579/Z/19/Z

Revision History  

• Version 1.0: 2022-08-03
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description