6GO1

Crystal Structure of a Bacillus anthracis peptidoglycan deacetylase

• PDB DOI: https://doi.org/10.2210/pdb6GO1/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus anthracis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-01 Released: 2019-04-10 
• Deposition Author(s): Giastas, P., Andreou, A., Eliopoulos, E.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.245 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

The putative polysaccharide deacetylase Ba0331: cloning, expression, crystallization and structure determination.

Andreou, A., Giastas, P., Arnaouteli, S., Tzanodaskalaki, M., Tzartos, S.J., Bethanis, K., Bouriotis, V., Eliopoulos, E.E.

(2019) Acta Crystallogr F Struct Biol Commun 75: 312-320

• PubMed: 30950833 
• DOI: https://doi.org/10.1107/S2053230X19001766
• Primary Citation of Related Structures:  
  6GO1


• PubMed Abstract: 
  

  Ba0331 is a putative polysaccharide deacetylase from Bacillus anthracis, the etiological agent of the disease anthrax, that contributes to adaptation of the bacterium under extreme conditions and to maintenance of the cell shape. In the present study, the crystal structure of Ba0331 was determined at 2.6 Å resolution. The structure consists of two domains: a fibronectin type 3-like (Fn3-like) domain and a NodB catalytic domain. The latter is present in all carbohydrate esterase family 4 enzymes, while a comparative analysis of the Fn3-like domain revealed structural plasticity despite the retention of the conserved Fn3-like domain characteristics.

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Organizational Affiliation: 

Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 74.4 kDa 
• Atom Count: 5,294 
• Modelled Residue Count: 636 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polysaccharide deacetylase-like protein	A, B	318	Bacillus anthracis	Mutation(s): 0  Gene Names: yxkH, BA_0331, BASH2_05488
UniProt
Find proteins for A0A3P1TYX8 (Bacillus anthracis) Explore A0A3P1TYX8  Go to UniProtKB:  A0A3P1TYX8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], J [auth B], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	D [auth A], I [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.245 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.723	α = 90
b = 211.795	β = 91.82
c = 46.784	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Giastas, P., Andreou, A., Eliopoulos, E.E.

Revision History  

• Version 1.0: 2019-04-10
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description