7XRO | pdb_00007xro

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

• PDB DOI: https://doi.org/10.2210/pdb7XRO/pdb

• Classification: TRANSCRIPTION
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-05-10 Released: 2023-05-17 
• Deposition Author(s): Ki, N., Ha, N.-C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

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.

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)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 45.58 kDa 
• Atom Count: 3,186 
• Modeled Residue Count: 410 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RipR	A [auth B], B [auth C]	208	Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344	Mutation(s): 0  Gene Names: stmR, hcaR_2
UniProt
Find proteins for Q9RQ20 (Salmonella typhimurium) Explore Q9RQ20  Go to UniProtKB:  Q9RQ20

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HCI (Subject of Investigation/LOI)	D [auth B]	HYDROCINNAMIC ACID C9 H10 O2 XMIIGOLPHOKFCH-UHFFFAOYSA-N
GLY	C [auth B], G [auth C]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
CL	E [auth B], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.107	α = 90
b = 83.107	β = 90
c = 172.199	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Ki, N., Ha, N.-C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• 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