Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.60 kDa 
• Atom Count: 4659 
• Modelled Residue Count: 584 
• Deposited Residue Count: 587 
• Unique protein chains: 1

4QX2

Cry3A Toxin structure obtained by injecting Bacillus thuringiensis cells in an XFEL beam, collecting data by serial femtosecond crystallographic methods and processing data with the cctbx.xfel software suite

• PDB DOI: 10.2210/pdb4QX2/pdb

• Classification: TOXIN
• Organism(s): Bacillus thuringiensis serovar tenebrionis
• Expression System: Bacillus thuringiensis serovar israelensis
• Mutation(s): No 


• Deposited: 2014-07-17 Released: 2014-08-13 
• Deposition Author(s): Sawaya, M.R., Cascio, D., Gingery, M., Rodriguez, J., Goldschmidt, L., Colletier, J.-P., Messerschmidt, M., Boutet, S., Koglin, J.E., Williams, G.J., Brewster, A.S., Nass, K., Hattne, J., Botha, S., Doak, R.B., Shoeman, R.L., DePonte, D.P., Park, H.-W., Federici, B.A., Sauter, N.K., Schlichting, I., Eisenberg, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.201 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

Protein crystal structure obtained at 2.9 angstrom resolution from injecting bacterial cells into an X-ray free-electron laser beam.

Sawaya, M.R., Cascio, D., Gingery, M., Rodriguez, J., Goldschmidt, L., Colletier, J.P., Messerschmidt, M.M., Boutet, S., Koglin, J.E., Williams, G.J., Brewster, A.S., Nass, K., Hattne, J., Botha, S., Doak, R.B., Shoeman, R.L., DePonte, D.P., Park, H.W., Federici, B.A., Sauter, N.K., Schlichting, I., Eisenberg, D.S.

(2014) Proc Natl Acad Sci U S A 111: 12769-12774

• PubMed: 25136092 
• DOI: 10.1073/pnas.1413456111
• Primary Citation of Related Structures:  
  4QX0, 4QX1, 4QX2, 4QX3


• PubMed Abstract: 
  

It has long been known that toxins produced by Bacillus thuringiensis (Bt) are stored in the bacterial cells in crystalline form. Here we describe the structure determination of the Cry3A toxin found naturally crystallized within Bt cells. When whole Bt cells were streamed into an X-ray free-electron laser beam we found that scattering from other cell components did not obscure diffraction from the crystals. The resolution limits of the best diffraction images collected from cells were the same as from isolated crystals. The integrity of the cells at the moment of diffraction is unclear; however, given the short time (∼ 5 µs) between exiting the injector to intersecting with the X-ray beam, our result is a 2.9-Å-resolution structure of a crystalline protein as it exists in a living cell. The study suggests that authentic in vivo diffraction studies can produce atomic-level structural information.

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Organizational Affiliation: 

UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095-1570; [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pesticidal crystal protein cry3Aa	A	587	Bacillus thuringiensis serovar tenebrionis	Mutation(s): 0  Gene Names: bt13, cry3A, cry3Aa, cryC, cryIIIa, cryIIIA(a)
UniProt
Find proteins for P0A379 (Bacillus thuringiensis subsp. tenebrionis) Explore P0A379  Go to UniProtKB:  P0A379

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.201 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.05	α = 90
b = 134.76	β = 90
c = 104.85	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
cctbx.xfel	data reduction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-07-17 
• Released Date: 2014-08-13 
Deposition Author(s): Sawaya, M.R., Cascio, D., Gingery, M., Rodriguez, J., Goldschmidt, L., Colletier, J.-P., Messerschmidt, M., Boutet, S., Koglin, J.E., Williams, G.J., Brewster, A.S., Nass, K., Hattne, J., Botha, S., Doak, R.B., Shoeman, R.L., DePonte, D.P., Park, H.-W., Federici, B.A., Sauter, N.K., Schlichting, I., Eisenberg, D.

Revision History  

• Version 1.0: 2014-08-13
  Type: Initial release
  
• Version 1.1: 2014-09-03
  Changes: Database references
• Version 1.2: 2014-09-24
  Changes: Database references
• Version 1.3: 2018-02-14
  Changes: Data collection