8AD6

Structure of DarB bound to c-di-AMP

• PDB DOI: https://doi.org/10.2210/pdb8AD6/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2022-07-07 Released: 2023-07-19 
• Deposition Author(s): Garcia-Pino, A., Talavera, A.
• Funding Organization(s): Fonds National de la Recherche Scientifique (FNRS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.194 
• R-Value Work: 0.174 

Literature

Structure of DarB bound to c-di-AMP

Garcia-Pino, A., Talavera, A.

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

Macromolecule Content

• Total Structure Weight: 34.62 kDa 
• Atom Count: 2,550 
• Modelled Residue Count: 275 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CBS domain-containing protein	A, B	147	Bacillus subtilis	Mutation(s): 0  Gene Names: B4417_3749, Bateq7PJ16_1575, C6Y43_13715, FAL52_03995
UniProt
Find proteins for O31698 (Bacillus subtilis (strain 168)) Explore O31698  Go to UniProtKB:  O31698

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2BA (Subject of Investigation/LOI)	C [auth A], D [auth B]	(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide C20 H24 N10 O12 P2 PDXMFTWFFKBFIN-XPWFQUROSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.194 
• R-Value Work: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.617	α = 90
b = 42.293	β = 90
c = 64.974	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-19 
Deposition Author(s): Garcia-Pino, A., Talavera, A.

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Funding Organization	Location	Grant Number
Fonds National de la Recherche Scientifique (FNRS)	Belgium	T.0066.18

Revision History  

• Version 1.0: 2023-07-19
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description