7V5V | pdb_00007v5v

LysR family transcriptional regulator RipR from Salmonella Typhimurium

• PDB DOI: https://doi.org/10.2210/pdb7V5V/pdb

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


• Deposited: 2021-08-18 Released: 2022-08-24 
• 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: 2.37 Å
• R-Value Free: 
  0.295 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: in silico

Literature

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

Ki, N.

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: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.55 kDa 
• Atom Count: 6,309 
• Modeled Residue Count: 822 
• Deposited Residue Count: 832 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RipR	A, B, C, D	208	Salmonella enterica subsp. enterica serovar Enteritidis	Mutation(s): 0  Gene Names: stmR
UniProt
Find proteins for H9L457 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore H9L457  Go to UniProtKB:  H9L457

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.295 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.405	α = 90
b = 72.415	β = 104.62
c = 91.612	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Ki, N., Ha, N.-C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description