1M1F | pdb_00001m1f

Kid toxin protein from E.coli plasmid R1

• PDB DOI: https://doi.org/10.2210/pdb1M1F/pdb

• Classification: TOXIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-06-19 Released: 2002-11-20 
• Deposition Author(s): Hargreaves, D., Santos-Sierra, S., Giraldo, R., Sabariegos-Jareno, R., de la Cueva-Mendez, G., Boelens, R., Diaz-Orejas, R., Rafferty, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.182 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Structural and Functional Analysis of the Kid toxin protein from E.coli plasmid R1

Hargreaves, D., Santos-Sierra, S., Giraldo, R., Sabariegos-Jareno, R., de la Cueva-Mendez, G., Boelens, R., Diaz-Orejas, R., Rafferty, J.B.

(2002) Structure 10: 1425-1433

• PubMed: 12377128 
• DOI: https://doi.org/10.1016/s0969-2126(02)00856-0
• Primary Citation Related Structures: 
  1M1F


• PubMed Abstract: 
  

  We have determined the structure of Kid toxin protein from E. coli plasmid R1 involved in stable plasmid inheritance by postsegregational killing of plasmid-less daughter cells. Kid forms a two-component system with its antagonist, Kis antitoxin. Our 1.4 A crystal structure of Kid reveals a 2-fold symmetric dimer that closely resembles the DNA gyrase-inhibitory toxin protein CcdB from E. coli F plasmid despite the lack of any notable sequence similarity. Analysis of nontoxic mutants of Kid suggests a target interaction interface associated with toxicity that is in marked contrast to that proposed for CcdB. A possible region for interaction of Kid with the antitoxin is proposed that overlaps with the target binding site and may explain the mode of antitoxin action.

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Organizational Affiliation: 
• Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 23.89 kDa 
• Atom Count: 2,009 
• Modeled Residue Count: 212 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kid toxin protein	A, B	110	Escherichia coli	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for P13976 (Escherichia coli) Explore P13976  Go to UniProtKB:  P13976

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.182 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.264	α = 90
b = 45.457	β = 96.12
c = 65.021	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CCP4	model building
REFMAC	refinement
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-20 
Deposition Author(s): Hargreaves, D., Santos-Sierra, S., Giraldo, R., Sabariegos-Jareno, R., de la Cueva-Mendez, G., Boelens, R., Diaz-Orejas, R., Rafferty, J.B.

Revision History  

• Version 1.0: 2002-11-20
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Advisory, Data collection, Database references, Derived calculations