7EI6 | pdb_00007ei6

GNRA tetraloop receptor motif composed of RNA and DNA

• PDB DOI: https://doi.org/10.2210/pdb7EI6/pdb
• NAKB: 7EI6

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

RNA GNRA tetraloop and tetraloop receptor motifs

Kondo, J., Hayasaka, A.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 11.71 kDa 
• Atom Count: 743 
• Modeled Residue Count: 35 
• Deposited Residue Count: 35 
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA/RNA (35-MER)	A	35	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IR3	B [auth A], C [auth A], D [auth A]	IRIDIUM (III) ION Ir MILUBEOXRNEUHS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.928	α = 90
b = 82.928	β = 90
c = 71.245	γ = 120

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., Hayasaka, A.

Revision History  

• Version 1.0: 2022-03-30
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description