7ECP | pdb_00007ecp

RNA duplex containing C-Ag-U

• PDB DOI: https://doi.org/10.2210/pdb7ECP/pdb
• NAKB: 7ECP

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

RNA duplex containing C-Ag-U

Kondo, J., Tsudura, A.

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: 15.7 kDa 
• Atom Count: 1,017 
• Modeled Residue Count: 48 
• Deposited Residue Count: 48 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth C], H [auth C]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.968	α = 90
b = 88.968	β = 90
c = 33.326	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

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

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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