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), 0.190 (DCC)
R-Value Work:
0.174 (Depositor), 0.170 (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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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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), 0.190 (DCC)
R-Value Work: 0.174 (Depositor), 0.170 (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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Ligand Structure Quality Assessment

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

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.