2D42 | pdb_00002d42

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.265 (Depositor), 0.264 (DCC)
R-Value Work:
0.230 (Depositor), 0.229 (DCC)
R-Value Observed:
0.230 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2D42

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/prot.20843
Primary Citation Related Structures:
2D42

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6L5X8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.265 (Depositor), 0.264 (DCC)
R-Value Work: 0.230 (Depositor), 0.229 (DCC)
R-Value Observed: 0.230 (Depositor)

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-01-17

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.