5URP | pdb_00005urp

Plx2a, an ADP-ribosyltransferase toxin from Paenibacillus larvae

• PDB DOI: https://doi.org/10.2210/pdb5URP/pdb

• Classification: TOXIN
• Organism(s): Paenibacillus larvae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-02-12 Released: 2017-12-20 
• Deposition Author(s): Ravulapalli, R., Heney, K., Ebeling, J., Genersch, E., Merrill, A.R.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.200 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Structural and functional characterization of Plx2a, an ADP-ribosyltransferase toxin from Paenibacillus larvae

Ravulapalli, R., Heney, K., Ebeling, J., Genersch, E., Merrill, A.R.

(2017) Environ Microbiol 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 25.56 kDa 
• Atom Count: 1,789 
• Modeled Residue Count: 201 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin 2A	A	223	Paenibacillus larvae	Mutation(s): 0  Gene Names: plx2A
UniProt
Find proteins for M9V3B7 (Paenibacillus larvae) Explore M9V3B7  Go to UniProtKB:  M9V3B7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.200 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.92	α = 90
b = 53.97	β = 90
c = 98.18	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Ravulapalli, R., Heney, K., Ebeling, J., Genersch, E., Merrill, A.R.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-106661

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description