5D5L | pdb_00005d5l

PreQ1-II riboswitch with an engineered G-U wobble pair bound to Cs+

• PDB DOI: https://doi.org/10.2210/pdb5D5L/pdb
• NAKB: 5D5L

• Classification: RNA
• Organism(s): Lacticaseibacillus rhamnosus LOCK908
• Mutation(s): No 


• Deposited: 2015-08-10 Released: 2016-08-10 
• Deposition Author(s): Wedekind, J.E., Liberman, J.A., Salim, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.247 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Cesium(I) binding to G-U-wobble base pairs in preQ1 riboswitches with implications for crystallographic phasing

Belashov, I.A., Liberman, J.A., Salim, M., Wedekind, J.E.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 104.74 kDa 
• Atom Count: 6,871 
• Modeled Residue Count: 308 
• Deposited Residue Count: 308 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
PreQ1-II riboswitch	A, B, C, D	77	Lacticaseibacillus rhamnosus LOCK908

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRF	JA [auth B], QA [auth C], U [auth A], ZA [auth D]	7-DEAZA-7-AMINOMETHYL-GUANINE C7 H9 N5 O MEYMBLGOKYDGLZ-UHFFFAOYSA-N
CS	BA [auth B], CA [auth B], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], R [auth A], S [auth A], T [auth A], UA [auth D], VA [auth D], WA [auth D], XA [auth D], YA [auth D]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N
MG	AA [auth A], AB [auth D], BB [auth D], CB [auth D], KA [auth B], LA [auth B], MA [auth B], RA [auth C], SA [auth C], TA [auth C], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.247 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.358	α = 90
b = 57.833	β = 107.64
c = 99.493	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-2000	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Wedekind, J.E., Liberman, J.A., Salim, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM063162
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	RR026501

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description