1SAQ | pdb_00001saq

Crystal Structure of the RNA octamer GIC(GA)GCC

• PDB DOI: https://doi.org/10.2210/pdb1SAQ/pdb
• NAKB: 1SAQ

• Classification: RNA
• Mutation(s): No 


• Deposited: 2004-02-09 Released: 2004-05-18 
• Deposition Author(s): Jang, S.B., Baeyens, K., Jeong, M.S., SantaLucia Jr, J., Turner, D., Holbrook, S.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.297 (Depositor), 0.304 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.237 (DCC) 

Literature

Structures of two RNA octamers containing tandem G.A base pairs.

Jang, S.B., Baeyens, K., Jeong, M.S., SantaLucia, J., Turner, D., Holbrook, S.R.

(2004) Acta Crystallogr D Biol Crystallogr 60: 829-835

• PubMed: 15103128 
• DOI: https://doi.org/10.1107/S0907444904003804
• Primary Citation Related Structures: 
  1SA9, 1SAQ


• PubMed Abstract: 
  

  The crystal structures of two RNA octamers, 5'-GGC(GA)GCC-3' and 5'-GIC(GA)GCC-3', have been determined from X-ray diffraction data to 2.8 and 2.7 A resolution, respectively. The RNA octamers crystallize in isomorphous unit cells containing two mispairs arranged in a self-complementary manner and one single strand in the asymmetric unit. The single strand pairs with another single strand related by crystallographic symmetry to form a third unique double helix. Tandem non-Watson-Crick G.A/A.G base pairs of the sheared type comprise an internal loop in the middle of each duplex. The NMR structure of this octameric RNA sequence is also known, allowing comparison of the variation between the six crystallographic duplexes and the solution structure. In the symmetric duplex of the octamer containing inosine, the sheared G.A pairs incorporate a bound water molecule. This duplex also binds one water molecule per strand in the minor groove adjacent to the G.A pairs.

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Organizational Affiliation: 
• Korea Nanobiotechnology Center, Pusan National University, Busan 609-735, South Korea. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.83 kDa 
• Atom Count: 870 
• Modeled Residue Count: 40 
• Deposited Residue Count: 40 
• Unique nucleic acid chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.297 (Depositor), 0.304 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.237 (DCC) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.65	α = 90
b = 69.65	β = 90
c = 67.81	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-18 
Deposition Author(s): Jang, S.B., Baeyens, K., Jeong, M.S., SantaLucia Jr, J., Turner, D., Holbrook, S.R.

Revision History  

• Version 1.0: 2004-05-18
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references