7M3V | pdb_00007m3v

RNA bulged-G motif

• PDB DOI: https://doi.org/10.2210/pdb7M3V/pdb
• NAKB: 7M3V

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


• Deposited: 2021-03-19 Released: 2022-03-23 
• Deposition Author(s): Kondo, J., Sekiguchi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

RNA bulged-G motif

Kondo, J., Sekiguchi, S.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 8.94 kDa 
• Atom Count: 629 
• Modeled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.657	α = 90
b = 29.657	β = 90
c = 76.76	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: 2022-03-23 
Deposition Author(s): Kondo, J., Sekiguchi, S.

Revision History  

• Version 1.0: 2022-03-23
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description