4ARY | pdb_00004ary

Lepidopteran-specific toxin Cry1Ac in complex with receptor specificity determinant GalNAc

• PDB DOI: https://doi.org/10.2210/pdb4ARY/pdb

• Classification: TOXIN
• Organism(s): Bacillus thuringiensis serovar kurstaki
• Mutation(s): No 


• Deposited: 2012-04-27 Released: 2013-05-15 
• Deposition Author(s): Derbyshire, D.J., Carroll, J., Ellar, D.J., Li, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.244 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Structural Basis of Galnac-Dependent Receptor Recognition by B. Thuringiensis Toxin Cry1Ac

Derbyshire, D.J., Carroll, J., Ellar, D.J., Li, J.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 261.7 kDa 
• Atom Count: 18,492 
• Modeled Residue Count: 2,315 
• Deposited Residue Count: 2,324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PESTICIDAL CRYSTAL PROTEIN CRY1AC	A, B, C, D	581	Bacillus thuringiensis serovar kurstaki	Mutation(s): 0
UniProt
Find proteins for P05068 (Bacillus thuringiensis subsp. kurstaki) Explore P05068  Go to UniProtKB:  P05068

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NGA	E [auth A], G [auth B], I [auth C], J [auth D]	2-acetamido-2-deoxy-beta-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-JAJWTYFOSA-N
13D	F [auth A], H [auth B]	1,3-DIAMINOPROPANE C3 H10 N2 XFNJVJPLKCPIBV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.244 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.36	α = 90
b = 51.19	β = 105.75
c = 210.65	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-15 
Deposition Author(s): Derbyshire, D.J., Carroll, J., Ellar, D.J., Li, J.

Revision History  

• Version 1.0: 2013-05-15
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Database references
• Version 1.2: 2019-01-30
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary