1KR8

Refinement of d(GCGAAGC) Hairpin Structure Using One-and Two-Bonds Residual Dipolar Couplings

• PDB DOI: https://doi.org/10.2210/pdb1KR8/pdb
• NAKB: 1KR8
• BMRB: 5282

• Classification: DNA
• Mutation(s): No 


• Deposited: 2002-01-09 Released: 2002-12-11 
• Deposition Author(s): Padrta, P., Stefl, R., Zidek, L., Sklenar, V.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 14 
• Conformers Submitted: 14 
• Selection Criteria: all calculated structures submitted 

Literature

Refinement of d(GCGAAGC) Hairpin Structure Using One- and Two-Bond Residual Dipolar Couplings

Padrta, P., Stefl, R., Kralik, L., Zidek, L., Sklenar, V.

(2002) J Biomol NMR 24: 1-14

• PubMed: 12449414 
• DOI: https://doi.org/10.1023/a:1020632900961
• Primary Citation of Related Structures:  
  1KR8, 1PQT


• PubMed Abstract: 
  

  The structure of the 13C,15N-labeled d(GCGAAGC) hairpin, as determined by NMR spectroscopy and refined using molecular dynamics with NOE-derived distances, torsion angles, and residual dipolar couplings (RDCs), is presented. Although the studied molecule is of small size, it is demonstrated that the incorporation of diminutive RDCs can significantly improve local structure determination of regions undefined by the conventional restraints. Very good correlation between the experimental and back-calculated small one- and two-bond 1H-13C, 1H-15N, 13C-13C and 13C-15N coupling constants has been attained. The final structures clearly show typical features of the miniloop architecture. The structure is discussed in context of the extraordinary stability of the d(GCGAAGC) hairpin, which originates from a complex interplay between the aromatic base stacking and hydrogen bonding interactions.

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Organizational Affiliation: 

National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2.15 kDa 
• Atom Count: 143 
• Modelled Residue Count: 7 
• Deposited Residue Count: 7 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*AP*AP*GP*C)-3'	A	7	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 14 
• Conformers Submitted: 14 
• Selection Criteria: all calculated structures submitted 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-11 
Deposition Author(s): Padrta, P., Stefl, R., Zidek, L., Sklenar, V.

Revision History  

• Version 1.0: 2002-12-11
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations