6XKO

Class III PreQ1 riboswitch mutant A84G

PDB DOI: https://doi.org/10.2210/pdb6XKO/pdb
NAKB: 6XKO

Classification: RNA
Organism(s): Faecalibacterium prausnitzii
Mutation(s): No

Deposited: 2020-06-26 Released: 2021-12-29
Deposition Author(s): Srivastava, K.Y., Jenkins, J.L., Wedekind, J.E.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.223
R-Value Work: 0.208
R-Value Observed: 0.210

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

New insights into Class III PreQ1 metabolite binding

Srivastava, K.Y., Jenkins, J.L., Wedekind, J.E.

To be published.

Macromolecule Content

Total Structure Weight: 32.83 kDa
Atom Count: 2,057
Modelled Residue Count: 95
Deposited Residue Count: 101
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Class III PreQ1 riboswitch	A	101	Faecalibacterium prausnitzii
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRF Query on PRF 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]	7-DEAZA-7-AMINOMETHYL-GUANINE C₇ H₉ N₅ O MEYMBLGOKYDGLZ-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: 2.75 Å
R-Value Free: 0.223
R-Value Work: 0.208
R-Value Observed: 0.210
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.798	α = 90
b = 83.798	β = 90
c = 277.104	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-12-29

Deposition Author(s):

Srivastava, K.Y.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM63162-14

Revision History (Full details and data files)

Version 1.0: 2021-12-29
Type: Initial release
Version 1.1: 2023-10-18
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.