4RBY | pdb_00004rby

First X-ray structure of RNA containing guanosine phosphorodithioate

• PDB DOI: https://doi.org/10.2210/pdb4RBY/pdb
• NAKB: 4RBY

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


• Deposited: 2014-09-13 Released: 2015-09-16 
• Deposition Author(s): Pallan, P.S., Egli, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 
  0.213 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.168 (DCC) 

Starting Model: experimental

Literature

Crystal Structure, Stability and siRNA Activity of Phosphorodithioate-Modified RNAs

Pallan, P.S., Yang, X., Sierant, M., Abeydeera, N.D., Hassell, T., Martinez, C., Janicka, M., Nawrot, B., Egli, M.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 4.06 kDa 
• Atom Count: 358 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*CP*GP*CP*(2SG)P*AP*AP*UP*UP*AP*GP*CP*G)-3'	A	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SR	B [auth A], C [auth A]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free:  0.213 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.168 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.932	α = 90
b = 35.015	β = 128.8
c = 31.873	γ = 90

Software Package:

Software Name	Purpose
MD2	data collection
MOLREP	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-16 
Deposition Author(s): Pallan, P.S., Egli, M.

Revision History  

• Version 1.0: 2015-09-16
  Type: Initial release
  
• Version 1.1: 2017-07-12
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description