6Y0T

Sarcin Ricin Loop, mutant C2666A U2653G C2667A

• PDB DOI: https://doi.org/10.2210/pdb6Y0T/pdb
• NAKB: 6Y0T

• Classification: RNA
• Organism(s): synthetic construct
• Expression System: synthetic construct
• Mutation(s): No 


• Deposited: 2020-02-10 Released: 2021-02-17 
• Deposition Author(s): Ennifar, E., Westhof, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.203 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Sarcin Ricin Loop, mutant C2666A U2653G C2667A

Ennifar, E., Westhof, E.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.96 kDa 
• Atom Count: 1,583 
• Modelled Residue Count: 54 
• Deposited Residue Count: 54 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (27-MER)	A, B	27	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	C [auth A], D [auth A], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.203 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.17	α = 90
b = 23.96	β = 108.74
c = 63.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Ennifar, E., Westhof, E.

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Advisory, Data collection, Database references, Refinement description