2D95

LOW-TEMPERATURE STUDY OF THE A-DNA FRAGMENT D(GGGCGCCC)

• PDB DOI: https://doi.org/10.2210/pdb2D95/pdb
• NAKB: 2D95

• Classification: DNA
• Mutation(s): No 


• Deposited: 1993-07-13 Released: 1994-01-15 
• Deposition Author(s): Eisenstein, M., Hope, H., Haran, T.E., Frolow, F., Shakked, Z., Rabinovich, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 0.210 

Literature

Low-temperature study of the A-DNA fragment d(GGGCGCCC)

Eisenstein, M., Hope, H., Haran, T.E., Frolow, F., Shakked, Z., Rabinovich, D.

(1988) Acta Crystallogr B 44: 625-628

• PubMed: 3271557 
• DOI: https://doi.org/10.1107/s0108768188004732
• Primary Citation of Related Structures:  
  2D95


• PubMed Abstract: 
  

  The structure of the A-type duplex d(GGGCGCCC) was determined from data measured at 115 K to 2.0 A resolution. The space group, P4(3)2(1)2, is the same as for the 293 K structure; cell dimensions are a = 42.74 (4), c = 24.57 (1) A; R = 0.21 for 1694 observed reflections. The conformation and hydration are similar at the two temperatures. The average displacement parameters (B) for bases, sugars and phosphates all decrease by about 9 A2 relative to those found at 293 K. The individual values of B1/2 are linearly related to the distance from the molecular center of mass.

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Organizational Affiliation: 

Department of Structural Chemistry, Weizmann Institute of Science, Rehovot, Israel.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2.43 kDa 
• Atom Count: 201 
• Modelled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*C)-3')	A	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 0.210 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.74	α = 90
b = 42.74	β = 90
c = 24.57	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-15 
Deposition Author(s): Eisenstein, M., Hope, H., Haran, T.E., Frolow, F., Shakked, Z., Rabinovich, D.

Revision History  

• Version 1.0: 1994-01-15
  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: 2024-02-14
  Changes: Data collection, Database references