5L09 | pdb_00005l09

Crystal Structure of Quorum-Sensing Transcriptional Activator from Yersinia enterocolitica in complex with 3-oxo-N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide

• PDB DOI: https://doi.org/10.2210/pdb5L09/pdb

• Classification: TRANSCRIPTION
• Organism(s): Yersinia enterocolitica subsp. enterocolitica 8081
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-07-26 Released: 2016-09-07 
• Deposition Author(s): Kim, Y., Chhor, G., Jedrzejczak, R., Winans, S.C., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• 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: 2.00 Å
• R-Value Free: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Quorum-Sensing Transcriptional Activator from Yersinia enterocolitica

Kim, Y., Chhor, G., Jedrzejczak, R., Winans, S.C., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

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: 43.76 kDa 
• Atom Count: 2,947 
• Modeled Residue Count: 325 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Quorum-sensing transcriptional activator	A, B	179	Yersinia enterocolitica subsp. enterocolitica 8081	Mutation(s): 0  Gene Names: yenR, YE1599
UniProt
Find proteins for A1JMX7 (Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)) Explore A1JMX7  Go to UniProtKB:  A1JMX7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
482	C [auth A], K [auth B]	3-oxo-N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide C10 H15 N O4 YRYOXRMDHALAFL-QMMMGPOBSA-N
SO4	D [auth A], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], F [auth A], G [auth A], N [auth B], O [auth B], P [auth B], R [auth B], S [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	H [auth A], I [auth A], J [auth B], Q [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.878	α = 90
b = 122.775	β = 90
c = 107.603	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-07 
Deposition Author(s): Kim, Y., Chhor, G., Jedrzejczak, R., Winans, S.C., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	NIAID-DMID-NIHA12011124

Revision History  

• Version 1.0: 2016-09-07
  Type: Initial release
  
• Version 1.1: 2017-02-08
  Changes: Structure summary
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence, Database references, Other, Structure summary
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection
• Version 1.6: 2024-11-13
  Changes: Structure summary