6VEK | pdb_00006vek

Contact-dependent growth inhibition toxin-immunity protein complex from from E. coli 3006, full-length

PDB DOI: https://doi.org/10.2210/pdb6VEK/pdb

Classification: TOXIN
Organism(s): Escherichia coli 3006
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-01-02 Released: 2021-01-27
Deposition Author(s): Michalska, K., Stols, L., Eschenfeldt, W., Hayes, C.S., Goulding, C.W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI), Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.234 (Depositor), 0.237 (DCC)
R-Value Work:
0.182 (Depositor), 0.185 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Contact-dependent growth inhibition toxin-immunity protein complex from from E. coli 3006, full-length

Michalska, K., Stols, L., Eschenfeldt, W., Hayes, C.S., Goulding, C.W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)

To be published.

Macromolecule Content

Total Structure Weight: 55.83 kDa
Atom Count: 3,786
Modeled Residue Count: 474
Deposited Residue Count: 505
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
contact-dependent toxin CdiA	A	338	Escherichia coli 3006	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
contact-dependent immunity protein CdiI	B [auth I]	167	Escherichia coli 3006	Mutation(s): 0 Gene Names: BTQ06_14240
UniProt
Find proteins for A0A2A2C800 (Escherichia coli) Explore A0A2A2C800 Go to UniProtKB: A0A2A2C800
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2A2C800
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.234 (Depositor), 0.237 (DCC)
R-Value Work: 0.182 (Depositor), 0.185 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41	α = 90
b = 71.769	β = 90
c = 175.538	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-01-27

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM102318
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115586
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History (Full details and data files)

Version 1.0: 2021-01-27
Type: Initial release
Version 1.1: 2021-06-09
Changes: Experimental preparation
Version 1.2: 2021-08-18
Changes: Author supporting evidence, Database references, Structure summary
Version 1.3: 2023-10-11
Changes: Data collection, Refinement description
Version 1.4: 2024-11-13
Changes: Structure summary