8OWU

The crystal structure of the polymorphic toxin PT7(Bc) D37A mutant and its cognate immunity PIM7(Bc) complex

PDB DOI: https://doi.org/10.2210/pdb8OWU/pdb

Classification: TOXIN
Organism(s): Bacillus cereus BAG3X2-1
Expression System: Escherichia coli, Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-04-28 Released: 2024-06-19
Deposition Author(s): Tzarum, N., Fraenkel, R., Deouell, N., Cahana, I.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.264
R-Value Work: 0.214
R-Value Observed: 0.217

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Systematic Discovery of Antibacterial and Antifungal Bacterial Toxins

Nachmias, N., Dotan, N., Campos Rocha, M., Fraenkel, R., Detert, K., Kluzek, M., Shalom, M., Peedikayil-Kurien, S., Meitav, G., Rivitz, A., Shamash-Halevy, N., Cahana, I., Deouell, N., Klein, J., Schmidt, H., Oren-Suissa, M., Schlezinger, N., Oppenheimer-Shaanan, Y., Tzarum, N., Levy, A.

To be published.

Macromolecule Content

Total Structure Weight: 50.38 kDa
Atom Count: 3,174
Modelled Residue Count: 381
Deposited Residue Count: 424
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transposase	A [auth B], B [auth C]	95	Bacillus cereus BAG3X2-1	Mutation(s): 1 Gene Names: CN296_08810
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PIM7	C [auth D], D [auth E]	117	Bacillus cereus BAG3X2-1	Mutation(s): 0 Gene Names: CN296_08815
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.264
R-Value Work: 0.214
R-Value Observed: 0.217
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.607	α = 94.688
b = 51.912	β = 91.364
c = 54.52	γ = 101.675

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
PHASER	phasing
autoPROC	data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-06-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Israel	1600/21

Revision History (Full details and data files)

Version 1.0: 2024-06-19
Type: Initial release

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 R01GM133198.