401D | pdb_0000401d

STRUCTURE OF A DNA IN LOW SALT CONDITIONS D(GACCGCGGTC)

• PDB DOI: https://doi.org/10.2210/pdb401D/pdb
• NAKB: 401D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1998-06-02 Released: 1998-07-06 
• Deposition Author(s): Luo, M., Finley, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.285 (Depositor) 
• R-Value Work: 
  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

X-ray crystal structures of half the human papilloma virus E2 binding site: d(GACCGCGGTC).

Finley, J.B., Luo, M.

(1998) Nucleic Acids Res 26: 5719-5727

• PubMed: 9838004 
• DOI: https://doi.org/10.1093/nar/26.24.5719
• Primary Citation Related Structures: 
  348D, 349D, 401D


• PubMed Abstract: 
  

  The X-ray crystal structure of the DNA decamer d(GACCGCGGTC), containing half the human papilloma virus E2 binding site, has been solved from two crystals grown at different ionic conditions (50 mM MgCl2and 50 mM spermine or 1.56 mM MgCl2and 1.56 mM spermine). Despite the variation in salt concentration, the two DNA structures are in a very similar, A-type DNA conformation, with helical axes curving towards the major groove. Although the salt concentrations do not effect the helical parameters or hydration to a large degree, there is a change in the overall helical curvature; 18 degrees and 31 degrees for the low and high salt structures, respectively. This curvature appears to be sequence specific and biologically relevant when compared with similar DNA structures, including the E2 binding site of a protein-DNA complex.

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Organizational Affiliation: 
• Center for Macromolecular Crystallography, Department of Microbiology, University of Alabama-Birmingham, Birmingham, AL 35294-0005, USA. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.05 kDa 
• Atom Count: 236 
• Modeled Residue Count: 10 
• Deposited Residue Count: 10 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*CP*CP*GP*CP*GP*GP*TP*C)-3')	A	10	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.285 (Depositor) 
• R-Value Work:  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.444	α = 90
b = 38.444	β = 90
c = 80.175	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement
SAINT	data reduction
SAINT	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-07-06 
Deposition Author(s): Luo, M., Finley, J.B.

Revision History  

• Version 1.0: 1998-07-06
  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