5U0Q | pdb_00005u0q

RNA-DNA heptamer duplex with one 2'-5'-linkage

• PDB DOI: https://doi.org/10.2210/pdb5U0Q/pdb
• NAKB: 5U0Q

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


• Deposited: 2016-11-26 Released: 2017-11-29 
• Deposition Author(s): Luo, Z., Sheng, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.177 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

RNA-DNA heptamer duplex with one 2'-5'-linkage

Luo, Z., Sheng, J., Wang, R.

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: 8.96 kDa 
• Atom Count: 706 
• Modeled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 1
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')	A, C	7	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(*GP*GP*AP*GP*C)-D(P*T)-R(P*A)-3')	B, D	7	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	F [auth C]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
MG	E [auth B], G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.177 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.554	α = 90
b = 52.923	β = 96.05
c = 27.622	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-29 
Deposition Author(s): Luo, Z., Sheng, J.

Revision History  

• Version 1.0: 2017-11-29
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Author supporting evidence
• Version 1.2: 2018-03-28
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description