Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 59.06 kDa 
• Atom Count: 3906 
• Modelled Residue Count: 466 
• Deposited Residue Count: 522 
• Unique protein chains: 2

4ELY

CCDBVFI:GYRA14EC

• PDB DOI: 10.2210/pdb4ELY/pdb
• Entry: 4ELY supersedes: 3KU8

• Classification: TOXIN/ISOMERASE
• Organism(s): Shigella flexneri, Aliivibrio fischeri
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-11 Released: 2012-05-30 
• Deposition Author(s): De Jonge, N., Simic, R., Buts, L., Haesaerts, S., Roelants, K., Garcia-Pino, A., Sterckx, Y., De Greve, H., Lah, J., Loris, R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.217 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Alternative interactions define gyrase specificity in the CcdB family.

De Jonge, N., Simic, M., Buts, L., Haesaerts, S., Roelants, K., Garcia-Pino, A., Sterckx, Y., De Greve, H., Lah, J., Loris, R.

(2012) Mol Microbiol 84: 965-978

• PubMed: 22582791 
• DOI: 10.1111/j.1365-2958.2012.08069.x
• Primary Citation of Related Structures:  
  4ELY, 4ELZ


• PubMed Abstract: 
  

Toxin-antitoxin (TA) modules are small operons associated with stress response of bacteria. F-plasmid CcdB(F) was the first TA toxin for which its target, gyrase, was identified. Plasmidic and chromosomal CcdBs belong to distinct families. Conserved residues crucial for gyrase poisoning activity of plasmidic CcdBs are not conserved among these families. Here we show that the chromosomal CcdB(Vfi) from Vibrio fischeri is an active gyrase poison that interacts with its target via an alternative energetic mechanism. Changes in the GyrA14-binding surface of the Vibrio and F-plasmid CcdB family members illustrate neutral drift where alternative interactions can be used to achieve the same functionality. Differences in affinity between V. fischeri and F-plasmid CcdB for gyrase and their corresponding CcdA antitoxin possibly reflect distinct roles for TA modules located on plasmids and chromosomes.

---

Organizational Affiliation: 

Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit A	A, B	156	Shigella flexneri	Mutation(s): 0  Gene Names: gyrA, GYRASE, S2444, SF2311 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0AES5 (Shigella flexneri) Explore P0AES5  Go to UniProtKB:  P0AES5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CcdB	C, D	105	Aliivibrio fischeri	Mutation(s): 0  Gene Names: ccdB
UniProt
Find proteins for Q84B82 (Aliivibrio fischeri) Explore Q84B82  Go to UniProtKB:  Q84B82

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	F [auth A], G [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.217 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.073	α = 90
b = 90.833	β = 102.59
c = 58.13	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-11 
• Released Date: 2012-05-30 
Deposition Author(s): De Jonge, N., Simic, R., Buts, L., Haesaerts, S., Roelants, K., Garcia-Pino, A., Sterckx, Y., De Greve, H., Lah, J., Loris, R.
• This entry supersedes: 3KU8

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references