377D | pdb_0000377d

5'-R(*CP*GP*UP*AP*CP*DG)-3'

• PDB DOI: https://doi.org/10.2210/pdb377D/pdb
• NAKB: 377D

• Classification: RNA
• Mutation(s): No 


• Deposited: 1998-01-26 Released: 1998-08-10 
• Deposition Author(s): Biswas, R., Mitra, S.N., Sundaralingam, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.232 (Depositor) 
• R-Value Work: 
  0.188 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

1.76 A structure of a pyrimidine start alternating A-RNA hexamer r(CGUAC)dG.

Biswas, R., Mitra, S.N., Sundaralingam, M.

(1998) Acta Crystallogr D Biol Crystallogr 54: 570-576

• PubMed: 9761851 
• DOI: https://doi.org/10.1107/s0907444997013097
• Primary Citation Related Structures: 
  377D


• PubMed Abstract: 
  

  The crystal structure of the alternating RNA r(CGUAC)dG with a 3'-terminal deoxy G residue has been determined at 1.76 A resolution. The crystal belongs to the orthorhombic space group C2221, unit-cell dimensions a = 29.53, b = 44.61 and c = 94.18 A, with two independent duplexes (I and II) per asymmetric unit. The structure was solved by the molecular-replacement method. The final R factor was 18.8% using 4757 reflections in the resolution range 8.0-1.76 A. The model contains a total of 496 atoms and 85 solvent molecules. The two duplexes form the repeating unit and stack in the usual head-to-tail (5',3'/5',3') fashion into a pseudocontinuous helical column. Almost all of the 2'-hydroxyl groups are engaged in the three modes of water-mediated interactions to the base N3/O2 atoms, the sugar O4' atoms and the backbone phosphates. Thus, the 2'-hydroxyl group of RNA is probably contributing to the stability of the duplexes.

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Organizational Affiliation: 
• Biological Macromolecular Structure Center, Departments of Chemistry, Biochemistry and The Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.

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: 7.5 kDa 
• Atom Count: 581 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA-DNA (5'-R(*CP*GP*UP*AP*CP*DG)-3')	A, B, C, D	6	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.232 (Depositor) 
• R-Value Work:  0.188 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.53	α = 90
b = 44.61	β = 90
c = 94.18	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
R-AXIS	data reduction
R-AXIS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-08-10 
Deposition Author(s): Biswas, R., Mitra, S.N., Sundaralingam, M.

Revision History  

• Version 1.0: 1998-08-10
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2018-04-11
  Changes: Data collection
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references