7EI7 | pdb_00007ei7

RNA kink-turn motif with 2-aminopurine

• PDB DOI: https://doi.org/10.2210/pdb7EI7/pdb
• NAKB: 7EI7

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


• Deposited: 2021-03-30 Released: 2022-03-30 
• Deposition Author(s): Kondo, J., Saisu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.304 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Model: experimental

Literature

Structure-based design of a sequence-specific RNA probe that mimics the kink-turn motif

Miyauchi, T., Yamaguchi, K., Saisu, S., Kondo, J.

(2025) Nar Mol Med 2

• DOI: https://doi.org/10.1093/narmme/ugaf006

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 12.79 kDa 
• Atom Count: 836 
• Modeled Residue Count: 38 
• Deposited Residue Count: 38 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')	A, B	19	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.304 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.934	α = 90
b = 75.934	β = 90
c = 41.184	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-03-30 
Deposition Author(s): Kondo, J., Saisu, S.

Revision History  

• Version 1.0: 2022-03-30
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2025-04-16
  Changes: Database references, Structure summary