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

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
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A090IXS5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.