8OWS

The crystal structure of the polymorphic toxin PT1(Em) H44A mutant and its cognate immunity PIM1(Em) complex

PDB DOI: https://doi.org/10.2210/pdb8OWS/pdb

Classification: TOXIN
Organism(s): Escherichia marmotae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-04-28 Released: 2024-07-03
Deposition Author(s): Tzarum, N., Fraenkel, R., Deouell, N., Cahana, I.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.203
R-Value Work: 0.174
R-Value Observed: 0.175

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: 29.61 kDa
Atom Count: 2,165
Modelled Residue Count: 239
Deposited Residue Count: 257
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PIM1	A	122	Escherichia marmotae	Mutation(s): 0 Gene Names: C4A13_00008
UniProt
Find proteins for A0A370V6P8 (Escherichia marmotae) Explore A0A370V6P8 Go to UniProtKB: A0A370V6P8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A370V6P8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Type IV secretion protein Rhs	B [auth C]	135	Escherichia marmotae	Mutation(s): 1 Gene Names: C4A13_00009
UniProt
Find proteins for A0A370V6R2 (Escherichia marmotae) Explore A0A370V6R2 Go to UniProtKB: A0A370V6R2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A370V6R2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.203
R-Value Work: 0.174
R-Value Observed: 0.175
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.378	α = 90
b = 68.054	β = 90
c = 69.747	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
autoPROC	data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-07-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Israel	1600/21

Revision History (Full details and data files)

Version 1.0: 2024-07-03
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.