9AYU | pdb_00009ayu

Structure of the A type blood alpha-D-galactosamine galactosaminidase D463A mutant from Flavonifractor plautii

• PDB DOI: https://doi.org/10.2210/pdb9AYU/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Flavonifractor plautii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-08 Released: 2024-12-18 
• Deposition Author(s): Worrall, L.J., Strynadka, N.C.J.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.186 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Cobalt as a Cofactor for alpha-Galactosaminidase-Catalyzed Cleavage of Blood Group Antigens

Tian, Y., Worrall, L.J., Sim, L., Liu, F., Nasseri, S.A., Rahfeld, P., Mu, W., Kizhakkedathu, J.N., Strynadka, N.C.J., Withers, S.G.

(2024) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.4c03643

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 369.74 kDa 
• Atom Count: 28,603 
• Modeled Residue Count: 3,270 
• Deposited Residue Count: 3,360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A type blood alpha-D-galactosamine galactosaminidase	A, B, C, D, E	672	Flavonifractor plautii	Mutation(s): 0  EC: 3.2.1
UniProt
Find proteins for P0DTR5 (Flavonifractor plautii) Explore P0DTR5  Go to UniProtKB:  P0DTR5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	BA [auth D], F [auth A], HA [auth E], O [auth B], V [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	AA [auth C], EA [auth D], FA [auth D], GA [auth D], I [auth A], J [auth A], K [auth A], KA [auth E], L [auth A], LA [auth E], M [auth A], N [auth A], R [auth B], S [auth B], T [auth B], U [auth B], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	CA [auth D], G [auth A], IA [auth E], P [auth B], W [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	DA [auth D], H [auth A], JA [auth E], Q [auth B], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.186 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.326	α = 90
b = 164.29	β = 90.2
c = 131.763	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Worrall, L.J., Strynadka, N.C.J.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release