4Y13

SdiA in complex with octanoyl-rac-glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.096 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Mechanistic Roles of Novel Chemical Ligands on the SdiA Quorum-Sensing Transcription Regulator.

Nguyen, Y.Nguyen, N.X.Rogers, J.L.Liao, J.MacMillan, J.B.Jiang, Y.Sperandio, V.

(2015) Mbio 6: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional regulator of ftsQAZ gene cluster
A
246Escherichia coli O157:H7Mutation(s): 0 
Gene Names: sdiA
Find proteins for Q8XBD0 (Escherichia coli O157:H7)
Go to UniProtKB:  Q8XBD0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
480
Query on 480

Download SDF File 
Download CCD File 
A
(2S)-2,3-dihydroxypropyl octanoate
C11 H22 O4
GHBFNMLVSPCDGN-JTQLQIEISA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.096 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 129.857α = 90.00
b = 129.857β = 90.00
c = 125.680γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-04-15
    Type: Database references