6YJA | pdb_00006yja

DarB fom B. subtilis in complex with c-di-AMP

PDB DOI: https://doi.org/10.2210/pdb6YJA/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-04-02 Released: 2021-04-14
Deposition Author(s): Heidemann, J.L., Neumann, P., Ficner, R.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.210 (Depositor), 0.214 (DCC)
R-Value Work:
0.183 (Depositor), 0.186 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

DarB from B. subtilis

Heidemann, J.L., Neumann, P., Ficner, R.

To be published.

Macromolecule Content

Total Structure Weight: 34.79 kDa
Atom Count: 2,584
Modeled Residue Count: 276
Deposited Residue Count: 294
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CBS domain-containing protein YkuL	A, B	147	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: ykuL, BSU14130
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 4 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 G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [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 G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]