9FN5 | pdb_00009fn5

The REC domain (in the non-phosphorylated state) of XynC, a response regulator from G.proteiniphilus T-6

• PDB DOI: https://doi.org/10.2210/pdb9FN5/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Geobacillus proteiniphilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-09 Released: 2025-06-25 
• Deposition Author(s): Hadad, N., Lavid, N., Pazy, Y., Hiya, D., Shoham, Y., Shoham, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.247 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

The REC domain (in the non-phosphorylated state) of XynC, a response regulator from G.proteiniphilus T-6

Hadad, N., Lavid, N., Pazy, Y., Hiya, D., Shoham, Y., Shoham, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.65 kDa 
• Atom Count: 2,031 
• Modeled Residue Count: 249 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Two-component response regulator	A, B	133	Geobacillus proteiniphilus	Mutation(s): 0  Gene Names: xynC
UniProt
Find proteins for A0A090IXS5 (Caldibacillus thermoamylovorans) Explore A0A090IXS5  Go to UniProtKB:  A0A090IXS5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.247 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.737	α = 90
b = 125.737	β = 90
c = 39.087	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Hadad, N., Lavid, N., Pazy, Y., Hiya, D., Shoham, Y., Shoham, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release