1DC0

CRYSTAL STRUCTURE OF AN A/B-DNA INTERMEDIATE CATGGGCCCATG

• PDB DOI: https://doi.org/10.2210/pdb1DC0/pdb
• NAKB: 1DC0

• Classification: DNA
• Mutation(s): No 


• Deposited: 1999-11-03 Released: 2000-03-06 
• Deposition Author(s): Ng, H.L., Kopka, M.L., Dickerson, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.190 
• R-Value Work: 0.168 
• R-Value Observed: 0.172 

Literature

The structure of a stable intermediate in the A ;-> B DNA helix transition

Ng, H.L., Kopka, M.L., Dickerson, R.E.

(2000) Proc Natl Acad Sci U S A 97: 2035-2039

• PubMed: 10688897 
• DOI: https://doi.org/10.1073/pnas.040571197
• Primary Citation of Related Structures:  
  1DC0


• PubMed Abstract: 
  

  The DNA dodecamer CATGGGCCCATG in a crystal structure of resolution 1.3 A has a conformation intermediate between A and B DNA. This trapping of a stable intermediate suggests that the A and B DNA families are not discrete, as previously believed. The structure supports a base-centered rather than a backbone-centered mechanism for the A <--> B transition mediated by guanine tracts. Interconversion between A and B DNA provides another means for regulating protein-DNA recognition.

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Organizational Affiliation: 

Molecular Biology Institute, University of California, Los Angeles, CA 90095-1570, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.33 kDa 
• Atom Count: 579 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*TP*GP*GP*GP*CP*CP*CP*AP*TP*G)-3')	A, B	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.190 
• R-Value Work: 0.168 
• R-Value Observed: 0.172 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.197	α = 90
b = 40.197	β = 90
c = 77.336	γ = 90

Software Package:

Software Name	Purpose
DM	model building
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-03-06 
Deposition Author(s): Ng, H.L., Kopka, M.L., Dickerson, R.E.

Revision History  

• Version 1.0: 2000-03-06
  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: 2017-02-01
  Changes: Structure summary
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references