8AD6 | pdb_00008ad6

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free:
0.194 (Depositor), 0.194 (DCC)
R-Value Work:
0.174 (Depositor), 0.174 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of DarB bound to c-di-AMP

Garcia-Pino, A., Talavera, A.

To be published.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O31698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2BA (Subject of Investigation/LOI) Query on 2BA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	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		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: 1.52 Å
R-Value Free: 0.194 (Depositor), 0.194 (DCC)
R-Value Work: 0.174 (Depositor), 0.174 (DCC)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-19

Deposition Author(s):

Garcia-Pino, A.

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

Revision History (Full details and data files)

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

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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.