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)

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Experimental Data Snapshot

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

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

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

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.234 (Depositor) 
• R-Value Work:  0.182 (Depositor) 
• 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

Currently 6VEK does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 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)

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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  

• 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