7OXS | pdb_00007oxs

1.91 A crystal structure of DNA/2'-O-methyl-RNA heteroduplex

• PDB DOI: https://doi.org/10.2210/pdb7OXS/pdb
• NAKB: 7OXS

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


• Deposited: 2021-06-23 Released: 2021-07-14 
• Deposition Author(s): Dolot, R.M., Maciaszek, A., Nawrot, B.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

First High-Resolution Crystal Structures of DNA:2'-O-Methyl-RNA Heteroduplexes

Dolot, R., Maciaszek, A., Mikolajczyk, B., Nawrot, B.

(2022) Crystals (Basel) 

• DOI: https://doi.org/10.3390/cryst12060760

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.65 kDa 
• Atom Count: 849 
• Modeled Residue Count: 36 
• Deposited Residue Count: 36 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*CP*TP*CP*CP*TP*AP*G)-3')	A, C	9	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*(OMC)P*(OMU)P*(A2M)P*(OMG)P*(OMG)P*(A2M)P*(OMG)P*(A2M)P*(OMC))-3')	B, D	9	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	E [auth A], F [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.13	α = 90
b = 56.13	β = 90
c = 76.26	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Dolot, R.M., Maciaszek, A., Nawrot, B.C.

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2022-06-08
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description