9EBV | pdb_00009ebv

Structure of the Bacillus subtilis yjdF riboswitch aptamer domain in complex with lumichrome

PDB DOI: https://doi.org/10.2210/pdb9EBV/pdb

Classification: RNA
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Mutation(s): No

Deposited: 2024-11-13 Released: 2025-11-19
Deposition Author(s): Batey, R.T., Spradlin, S.F.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.246 (Depositor), 0.247 (DCC)
R-Value Work:
0.216 (Depositor), 0.216 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of the Bacillus subtilis yjdF riboswitch aptamer domain in complex with lumichrome

Batey, R.T., Spradlin, S.F.

To be published.

Macromolecule Content

Total Structure Weight: 53.43 kDa
Atom Count: 3,600
Modeled Residue Count: 162
Deposited Residue Count: 162
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (81-MER)	A, B [auth M]	81	Bacillus subtilis subsp. subtilis str. 168
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LUM (Subject of Investigation/LOI) Query on LUM Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain U [auth M] MOL2 format, chain K [auth A] MOL2 format, chain U [auth M] mmCIF format, chain K [auth A] mmCIF format, chain U [auth M]	K [auth A], U [auth M]	LUMICHROME C₁₂ H₁₀ N₄ O₂ ZJTJUVIJVLLGSP-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain U [auth M] Interactions & Density Focus chain K [auth A] Focus chain U [auth M]
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain R [auth M] SDF format, chain S [auth M] SDF format, chain T [auth M] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain R [auth M] MOL2 format, chain S [auth M] MOL2 format, chain T [auth M] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain R [auth M] mmCIF format, chain S [auth M] mmCIF format, chain T [auth M]	G [auth A] H [auth A] I [auth A] J [auth A] R [auth M] G [auth A], H [auth A], I [auth A], J [auth A], R [auth M], S [auth M], T [auth M]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth M] Focus chain S [auth M] Focus chain T [auth M] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth M] Focus chain S [auth M] Focus chain T [auth M]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth M] SDF format, chain M SDF format, chain N [auth M] SDF format, chain O [auth M] SDF format, chain P [auth M] SDF format, chain Q [auth M] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth M] MOL2 format, chain M MOL2 format, chain N [auth M] MOL2 format, chain O [auth M] MOL2 format, chain P [auth M] MOL2 format, chain Q [auth M] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth M] mmCIF format, chain M mmCIF format, chain N [auth M] mmCIF format, chain O [auth M] mmCIF format, chain P [auth M] mmCIF format, chain Q [auth M]	C [auth A] D [auth A] E [auth A] F [auth A] L [auth M] C [auth A], D [auth A], E [auth A], F [auth A], L [auth M], M, N [auth M], O [auth M], P [auth M], Q [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth M] Focus chain M Focus chain N [auth M] Focus chain O [auth M] Focus chain P [auth M] Focus chain Q [auth M] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth M] Focus chain M Focus chain N [auth M] Focus chain O [auth M] Focus chain P [auth M] Focus chain Q [auth M]