402D | pdb_0000402d

5'-R(*CP*GP*CP*CP*AP*GP*CP*G)-3'

• PDB DOI: https://doi.org/10.2210/pdb402D/pdb
• NAKB: 402D

• Classification: RNA
• Mutation(s): No 


• Deposited: 1998-06-04 Released: 1998-06-16 
• Deposition Author(s): Jang, S.B., Hung, L.-W., Chi, Y.-I., Holbrook, E.L., Carter, R., Holbrook, S.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.263 (Depositor) 
• R-Value Work: 
  0.207 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Structure of an RNA internal loop consisting of tandem C-A+ base pairs.

Jang, S.B., Hung, L.W., Chi, Y.I., Holbrook, E.L., Carter, R.J., Holbrook, S.R.

(1998) Biochemistry 37: 11726-11731

• PubMed: 9718295 
• DOI: https://doi.org/10.1021/bi980758j
• Primary Citation of Related Structures:  
  402D


• PubMed Abstract: 
  

  The crystal structure of the RNA octamer 5'-CGC(CA)GCG-3' has been determined from X-ray diffraction data to 2.3 A resolution. In the crystal, this oligomer forms a self-complementary double helix in the asymmetric unit. Tandem non-Watson-Crick C-A and A-C base pairs comprise an internal loop in the middle of the duplex, which is incorporated with little distortion of the A-form double helix. From the geometry of the C-A base pairs, it is inferred that the adenosine imino group is protonated and donates a hydrogen bond to the carbonyl group of the cytosine. The wobble geometry of the C-A+ base pairs is very similar to that of the common U-G non-Watson-Crick pair.

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Organizational Affiliation: 

Structural Biology Department, Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley 94720, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.08 kDa 
• Atom Count: 366 
• Modelled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique nucleic acid chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.263 (Depositor) 
• R-Value Work:  0.207 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.737	α = 90
b = 42.737	β = 90
c = 123.9	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-06-16 
Deposition Author(s): Jang, S.B., Hung, L.-W., Chi, Y.-I., Holbrook, E.L., Carter, R., Holbrook, S.R.

Revision History  

• Version 1.0: 1998-06-16
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references