7AB3

Crystal structure of the Escherichia coli toxin-antitoxin system HipBST (HipT S57A)

• PDB DOI: https://doi.org/10.2210/pdb7AB3/pdb

• Classification: TOXIN
• Organism(s): Escherichia coli O127:H6 str. E2348/69
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-09-06 Released: 2022-01-12 
• Deposition Author(s): Baerentsen, R.L., Brodersen, D.E.
• Funding Organization(s): Novo Nordisk Foundation, Danish National Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.236 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Starting Models: experimental

Literature

Structural basis for regulation of a tripartite toxin-antitoxin system by dual phosphorylation

Baerentsen, R.L., Nielsen, S.V., Lyngso, J., Bisiak, F., Pedersen, J.S., Gerdes, K., Sorensen, M.A., Brodersen, D.E.

(2022) bioRxiv 

• DOI: https://doi.org/10.1101/2022.01.28.478185

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

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

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 125.92 kDa 
• Atom Count: 8,668 
• Modelled Residue Count: 1,015 
• Deposited Residue Count: 1,102 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted transcriptional regulator, XRE family	A, D	107	Escherichia coli O127:H6 str. E2348/69	Mutation(s): 0  Gene Names: E2348C_3787
UniProt
Find proteins for B7UL98 (Escherichia coli O127:H6 (strain E2348/69 / EPEC)) Explore B7UL98  Go to UniProtKB:  B7UL98

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Couple_hipA domain-containing protein	B, E	103	Escherichia coli O127:H6 str. E2348/69	Mutation(s): 0  Gene Names: E2348C_3786
UniProt
Find proteins for B7UL97 (Escherichia coli O127:H6 (strain E2348/69 / EPEC)) Explore B7UL97  Go to UniProtKB:  B7UL97

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HipA_C domain-containing protein	C, F	341	Escherichia coli O127:H6 str. E2348/69	Mutation(s): 1  Gene Names: E2348C_3785
UniProt
Find proteins for B7UL96 (Escherichia coli O127:H6 (strain E2348/69 / EPEC)) Explore B7UL96  Go to UniProtKB:  B7UL96

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	C, F	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.236 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 281.68	α = 90
b = 106.07	β = 90.648
c = 57.56	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-12 
Deposition Author(s): Baerentsen, R.L., Brodersen, D.E.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF18OC0030646
Danish National Research Foundation	Denmark	DNRF120

Revision History  

• Version 1.0: 2022-01-12
  Type: Initial release
  
• Version 1.1: 2022-08-03
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary