6XKN

Class III PreQ1 riboswitch mutant A52G

• PDB DOI: https://doi.org/10.2210/pdb6XKN/pdb
• NAKB: 6XKN

• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 0.247 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 

Starting Model: experimental

Literature

New insights into Class III PreQ1 metabolite binding

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

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 32.83 kDa 
• Atom Count: 2,075 
• Modelled Residue Count: 96 
• Deposited Residue Count: 101 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRF (Subject of Investigation/LOI)	B [auth A]	7-DEAZA-7-AMINOMETHYL-GUANINE C7 H9 N5 O MEYMBLGOKYDGLZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 0.247 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.137	α = 90
b = 80.137	β = 90
c = 281.457	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-29 
Deposition Author(s): Srivastava, K.Y., Jenkins, J.L., Wedekind, J.E.

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

Revision History  

• Version 1.0: 2021-12-29
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 2.0: 2024-06-19
  Type: Coordinate replacement
  Reason: Model orientation/position
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary