9CYS

Toxin/immunity complex for a T6SS lipase effector from E. cloacae

• PDB DOI: https://doi.org/10.2210/pdb9CYS/pdb

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


• Deposited: 2024-08-02 Released: 2024-08-14 
• Deposition Author(s): Cuthbert, B.J., Jensen, S.J., Goulding, C.W., Hayes, C.S.
• Funding Organization(s): 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: 1.75 Å
• R-Value Free: 0.212 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Literature

Advanced glycation end-product (AGE) crosslinking activates a type 6 secretion system phospholipase effector protein

Jensen, S.J., Cuthbert, B.J., Garza-Sanchez, F., Helou, C.C., de Miranda, R., Goulding, C.W., Hayes, C.S.

(2024) Nature Communications 

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: 59.92 kDa 
• Atom Count: 4,363 
• Modelled Residue Count: 506 
• Deposited Residue Count: 543 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ankyrin repeat domain-containing protein	A [auth I]	230	Enterobacter cloacae	Mutation(s): 0
UniProt
Find proteins for A0A0H3CKN4 (Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCTC 10005 / WDCM 00083 / NCDC 279-56)) Explore A0A0H3CKN4  Go to UniProtKB:  A0A0H3CKN4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T6SS lipase effector	B [auth A]	313	Enterobacter cloacae	Mutation(s): 0  Gene Names: NCTC10005_04014
UniProt
Find proteins for A0A0M7ENE2 (Enterobacter cloacae) Explore A0A0M7ENE2  Go to UniProtKB:  A0A0M7ENE2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
PGE	E [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	D [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MIE (Subject of Investigation/LOI)	G [auth A]	methylglyoxal C3 H4 O2 AIJULSRZWUXGPQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.212 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.081	α = 90
b = 111.739	β = 90
c = 119.337	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-14 
Deposition Author(s): Cuthbert, B.J., Jensen, S.J., Goulding, C.W., Hayes, C.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	GM117930

Revision History  

• Version 1.0: 2024-08-14
  Type: Initial release