6ZOI | pdb_00006zoi

A lid blocking mechanism of a cone snail toxin revealed at the atomic level

• PDB DOI: https://doi.org/10.2210/pdb6ZOI/pdb

• Classification: TOXIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli 5-172-05_S1_C3
• Mutation(s): No 


• Deposited: 2020-07-07 Released: 2021-07-14 
• Deposition Author(s): Saikia, C., Altman-Gueta, H., Dym, O., Frolow, F., Gurevitz, M., Gordon, D., Reuveny, E., Karbat, I.
• Funding Organization(s): Israel Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.218 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

A lid blocking mechanism of a cone snail toxin revealed at the atomic level

Saikia, C., Altman-Gueta, H., Dym, O., Frolow, F., Gurevitz, M., Gordon, D., Reuveny, E., Karbat, I.

To be published.

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.71 kDa 
• Atom Count: 3,034 
• Modeled Residue Count: 359 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conknunitzin-C3 mutante	A, B, C, D, E, F	60	Escherichia coli K-12	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.218 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.855	α = 90
b = 90.327	β = 105.28
c = 44.645	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Saikia, C., Altman-Gueta, H., Dym, O., Frolow, F., Gurevitz, M., Gordon, D., Reuveny, E., Karbat, I.

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Funding Organization	Location	Grant Number
Israel Science Foundation	Israel	1248/15

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary