333D | pdb_0000333d

THE CRYSTAL STRUCTURE OF AN RNA OLIGOMER INCORPORATING TANDEM ADENOSINE-INOSINE MISMATCHES

• PDB DOI: https://doi.org/10.2210/pdb333D/pdb
• NAKB: 333D

• Classification: RNA
• Mutation(s): No 


• Deposited: 1997-05-20 Released: 1997-10-16 
• Deposition Author(s): Carter, R.J., Baeyens, K.J., SantaLucia Jr., J., Turner, D.H., Holbrook, S.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 
  0.266 (Depositor) 
• R-Value Work: 
  0.246 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of an RNA oligomer incorporating tandem adenosine-inosine mismatches.

Carter, R.J., Baeyens, K.J., SantaLucia, J., Turner, D.H., Holbrook, S.R.

(1997) Nucleic Acids Res 25: 4117-4122

• PubMed: 9321667 
• DOI: https://doi.org/10.1093/nar/25.20.4117
• Primary Citation Related Structures: 
  333D


• PubMed Abstract: 
  

  The X-ray crystallographic structure of the RNA duplex [r(CGCAIGCG)]2 has been refined to 2.5 A. It shows a symmetric internal loop of two non-Watson-Crick base pairs which form in the middle of the duplex. The tandem A-I/I-A pairs are related by a crystallographic two-fold axis. Both A(anti)-I(anti) mismatches are in a head-to-head conformation forming hydrogen bonds using the Watson-Crick positions. The octamer duplexes stack above one another in the cell forming a pseudo-infinite helix throughout the crystal. A hydrated calcium ion bridges between the 3'-terminal of one molecule and the backbone of another. The tandem A-I mismatches are incorporated with only minor distortion to the backbone. This is in contrast to the large helical perturbations often produced by sheared G-A pairs in RNA oligonucleotides.

---

Organizational Affiliation: 
• Structural Biology Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.61 kDa 
• Atom Count: 177 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*GP*CP*AP*IP*GP*CP*G)-3')	A	8	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free:  0.266 (Depositor) 
• R-Value Work:  0.246 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.05	α = 90
b = 39.05	β = 90
c = 58.85	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
R-AXIS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-10-16 
Deposition Author(s): Carter, R.J., Baeyens, K.J., SantaLucia Jr., J., Turner, D.H., Holbrook, S.R.

Revision History  

• Version 1.0: 1997-10-16
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2024-02-21
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-04-03
  Changes: Refinement description