5L09

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Quorum-sensing transcriptional activator
A, B
179Yersinia enterocolitica subsp. enterocolitica 8081Mutation(s): 0 
Gene Names: yenRYE1599
UniProt
Find proteins for A1JMX7 (Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081))
Explore A1JMX7 
Go to UniProtKB:  A1JMX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1JMX7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
482
Query on 482

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
3-oxo-N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide
C10 H15 N O4
YRYOXRMDHALAFL-QMMMGPOBSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B],
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
N [auth B]
O [auth B]
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
Query on ACY

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth B],
Q [auth B]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.878α = 90
b = 122.775β = 90
c = 107.603γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesNIAID-DMID-NIHA12011124

Revision History  (Full details and data files)

  • 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