7ECJ | pdb_00007ecj

RNA duplex containing C-A base pairs

• PDB DOI: https://doi.org/10.2210/pdb7ECJ/pdb
• NAKB: 7ECJ

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


• Deposited: 2021-03-12 Released: 2022-03-16 
• Deposition Author(s): Kondo, J., Uchida, Y.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.283 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Literature

RNA duplex containing C-A base pairs

Kondo, J., Uchida, Y.

To be published.

Biological Assembly 1  

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

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 11.62 kDa 
• Atom Count: 756 
• Modeled Residue Count: 36 
• Deposited Residue Count: 36 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')	A, B, C	12	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.283 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.78	α = 90
b = 47.78	β = 90
c = 186.215	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-16 
Deposition Author(s): Kondo, J., Uchida, Y.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	24245037

Revision History  

• Version 1.0: 2022-03-16
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection