2D42

Crystal structure analysis of a non-toxic crystal protein from Bacillus thuringiensis

• PDB DOI: https://doi.org/10.2210/pdb2D42/pdb

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


• Deposited: 2005-10-05 Released: 2006-01-17 
• Deposition Author(s): Akiba, T., Higuchi, K., Mizuki, E., Ekino, K., Shin, T., Ohba, M., Kanai, R., Harata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.265 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 

Literature

Nontoxic crystal protein from Bacillus thuringiensis demonstrates a remarkable structural similarity to beta-pore-forming toxins

Akiba, T., Higuchi, K., Mizuki, E., Ekino, K., Shin, T., Ohba, M., Kanai, R., Harata, K.

(2006) Proteins 63: 243-248

• PubMed: 16400649 
• DOI: https://doi.org/10.1002/prot.20843
• Primary Citation of Related Structures:  
  2D42

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Organizational Affiliation: 

Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 55.13 kDa 
• Atom Count: 4,100 
• Modelled Residue Count: 498 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
non-toxic crystal protein	A, B	249	Bacillus thuringiensis	Mutation(s): 0
UniProt
Find proteins for Q6L5X8 (Bacillus thuringiensis serovar shandongiensis) Explore Q6L5X8  Go to UniProtKB:  Q6L5X8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.265 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 
• Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.38	α = 90
b = 95.38	β = 90
c = 130.727	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-17 
Deposition Author(s): Akiba, T., Higuchi, K., Mizuki, E., Ekino, K., Shin, T., Ohba, M., Kanai, R., Harata, K.

Revision History  

• Version 1.0: 2006-01-17
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references