8Q6N

Xanthin riboswitch in complex with oxypurinol

PDB DOI: https://doi.org/10.2210/pdb8Q6N/pdb
NAKB: 8Q6N

Classification: RNA
Organism(s): Ideonella sp. B508-1
Mutation(s): No

Deposited: 2023-08-14 Released: 2024-08-28
Deposition Author(s): Nar, H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free:
0.282 (Depositor), 0.270 (DCC)
R-Value Work:
0.237 (Depositor), 0.240 (DCC)
R-Value Observed:
0.239 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7elr

Literature

Artificial oxypurinol-responsive riboswitches for gene expression control in mammalian cells based on bacterial xanthine aptamers

Schnapp, G., Hartig, J., Nar, H.

To be published.

Macromolecule Content

Total Structure Weight: 15.06 kDa
Atom Count: 1,015
Modelled Residue Count: 46
Deposited Residue Count: 46
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Xanthin riboswitch NMT-46 (46-MER)	A	46	Ideonella sp. B508-1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
141 (Subject of Investigation/LOI) Query on 141 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	Oxypurinol C₅ H₄ N₄ O₂ HXNFUBHNUDHIGC-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free: 0.282 (Depositor), 0.270 (DCC)
R-Value Work: 0.237 (Depositor), 0.240 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.811	α = 90
b = 85.091	β = 90
c = 97.162	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-08-28
Type: Initial release

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.