9VXG | pdb_00009vxg

ROS-Sensing Transcription Factor YchJ Regulates the RssB-RpoS Pathway to Protect Salmonella Against Oxidative Attack by Macrophages

• PDB DOI: https://doi.org/10.2210/pdb9VXG/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-07-18 Released: 2025-08-06 
• Deposition Author(s): Yuan, X.L., Wang, W.W.
• Funding Organization(s): Other government

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.266 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

ROS-Sensing Transcription Factor YchJ Regulates the RssB-RpoS Pathway to Protect Salmonella Against Oxidative Attack by Macrophages

Wang, W.W., Yuan, X.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.67 kDa 
• Atom Count: 1,182 
• Modeled Residue Count: 147 
• Deposited Residue Count: 147 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0225 protein YchJ	A	131	Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S	Mutation(s): 0  Gene Names: ychJ, STM1755
UniProt
Find proteins for Q8ZP43 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZP43  Go to UniProtKB:  Q8ZP43

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0225 protein YchJ	B	16	Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S	Mutation(s): 0  Gene Names: ychJ, STM1755
UniProt
Find proteins for Q8ZP43 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZP43  Go to UniProtKB:  Q8ZP43

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.266 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.937	α = 90
b = 58.937	β = 90
c = 124.367	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Yuan, X.L., Wang, W.W.

---

Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release