6L0Y | pdb_00006l0y

Structure of dsRNA with G-U wobble base pairs

• PDB DOI: https://doi.org/10.2210/pdb6L0Y/pdb
• NAKB: 6L0Y

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


• Deposited: 2019-09-27 Released: 2020-09-30 
• Deposition Author(s): Kim, K.-H., Hwang, J., Kim, J.H., Son, K.-P., Jang, Y., Kim, M., Kang, S.-J., Lee, J.-O., Choi, B.-S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Structure of dsRNA with G-U wobble base pairs

Kim, K.-H., Hwang, J., Kim, J.H., Son, K.-P., Jang, Y., Kim, M., Kang, S.-J., Lee, J.-O., Choi, B.-S.

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: 14.09 kDa 
• Atom Count: 930 
• Modeled Residue Count: 44 
• Deposited Residue Count: 44 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*UP*AP*GP*AP*CP*GP*CP*UP*UP*CP*GP*GP*CP*GP*UP*UP*UP*GP*CP*C)-3')	A, B	22	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.08	α = 90
b = 45.08	β = 90
c = 354.13	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Kim, K.-H., Hwang, J., Kim, J.H., Son, K.-P., Jang, Y., Kim, M., Kang, S.-J., Lee, J.-O., Choi, B.-S.

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Funding Organization	Location	Grant Number
Other private	Korea, Republic Of	KDDF-201706-06

Revision History  

• Version 1.0: 2020-09-30
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description