7EFI | pdb_00007efi

RNA kink-turn motif composed of RNA, DNA and 2'-O-methyl RNA

• PDB DOI: https://doi.org/10.2210/pdb7EFI/pdb
• NAKB: 7EFI

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


• Deposited: 2021-03-21 Released: 2022-03-30 
• Deposition Author(s): Kondo, J., Nagashima, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

RNA kink-turn motif composed of RNA, DNA and 2'-O-methyl RNA

Kondo, J., Nagashima, M.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.27 kDa 
• Atom Count: 417 
• Modeled Residue Count: 19 
• Deposited Residue Count: 19 
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*(OMG)P*(OMG)P*(OMG))-D(P*GP*A)-R(P*GP*(OMC)P*(OMC))-3')	A	19	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.565	α = 90
b = 70.565	β = 90
c = 48.165	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., Nagashima, M.

Revision History  

• Version 1.0: 2022-03-30
  Type: Initial release
  
• Version 2.0: 2022-05-11
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2023-11-29
  Changes: Data collection, Refinement description