RCSB PDB - 7XRO: LysR-family transcriptional regulator RipR effector binding domain with its effector, 3-phenylpropionic acid

 7XRO

LysR-family transcriptional regulator RipR effector binding domain with its effector, 3-phenylpropionic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.218 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HCIClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

The activation mechanism of the itaconic acid-responsive LTTR RipR in the pathogenesis of the foodborne-pathogen Salmonella enterica

Ki, N.Ha, N.-C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RipRA [auth B],
B [auth C]
208Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344Mutation(s): 0 
Gene Names: stmRhcaR_2
UniProt
Find proteins for Q9RQ20 (Salmonella typhimurium)
Explore Q9RQ20 
Go to UniProtKB:  Q9RQ20
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RQ20
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.218 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.107α = 90
b = 83.107β = 90
c = 172.199γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HCIClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary