8HKH

Crystal structure of the LC/A1-DARPin18 complex

• PDB DOI: https://doi.org/10.2210/pdb8HKH/pdb

• Classification: TOXIN
• Organism(s): Clostridium botulinum, synthetic construct
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2022-11-26 Released: 2023-11-29 
• Deposition Author(s): Wu, Y., Leka, O., Kammerer, R.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.306 
• R-Value Work: 0.262 
• R-Value Observed: 0.264 

Literature

A DARPin Increases the Catalytic Activity of BoNT/A1

Leka, O., Wu, Y., Kammerer, R., Li, X., Plueckthun, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 132.72 kDa 
• Atom Count: 8,868 
• Modelled Residue Count: 1,108 
• Deposited Residue Count: 1,170 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BoNT/A	A, B	436	Clostridium botulinum	Mutation(s): 0  Gene Names: a
UniProt
Find proteins for P0DPI1 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)) Explore P0DPI1  Go to UniProtKB:  P0DPI1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed ankyrin repeat protein 18	C, D	149	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.306 
• R-Value Work: 0.262 
• R-Value Observed: 0.264 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.56	α = 74.98
b = 59.63	β = 89.9
c = 102.18	γ = 73.15

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Wu, Y., Leka, O., Kammerer, R.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A_163449
Swiss National Science Foundation	Switzerland	31003A_170028

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release