335D | pdb_0000335d

THE CRYSTAL STRUCTURE OF THE DNA DECAMER D(GGCAATTGCG) CONTAINS BOTH MAJOR AND MINOR GROOVE BINDING G.(G.C) TRIPLETS

• PDB DOI: https://doi.org/10.2210/pdb335D/pdb
• NAKB: 335D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1997-06-05 Released: 1998-08-10 
• Deposition Author(s): Nunn, C.M., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 
  0.203 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Structure of the DNA decamer d(GGCAATTGCG) contains both major- and minor-groove binding G.(G.C) base triplets.

Nunn, C.M., Neidle, S.

(1998) Acta Crystallogr D Biol Crystallogr 54: 577-583

• PubMed: 9761852 
• DOI: https://doi.org/10.1107/s090744499701559x
• Primary Citation Related Structures: 
  335D


• PubMed Abstract: 
  

  The crystal structure of the decamer d(GGCAATTGCG) has been determined at 2.4 A resolution. The central eight bases of each DNA single-strand base pair with a self-complementary strand to form an octamer B-DNA duplex. These duplexes lie end-to-end within the unit cell. The terminal 5'-G and G-3' bases of each decamer strand are unpaired, and interact with the neighbouring duplexes via interactions within both the major and minor groove. This results in base triplets of the type G-(G.C) and G*(G.C), with the third guanine base binding to a Watson-Crick G.C base pair from the major groove and the minor groove, respectively. The triplet interaction of the type G-(G.C) involves Hoogsteen hydrogen-bonding interactions between the two guanine bases. The minor- and major-groove base triplet interactions which exist within this structure act to stabilize the d(GCAATTGC)2 B-DNA octamer duplex.

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Organizational Affiliation: 
• The CRC Biomolecular Structure Unit, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, England. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.11 kDa 
• Atom Count: 272 
• 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*GP*CP*AP*AP*TP*TP*GP*CP*G)-3')	A	10	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work:  0.203 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.92	α = 90
b = 39.21	β = 90
c = 54.04	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-08-10 
Deposition Author(s): Nunn, C.M., Neidle, S.

Revision History  

• Version 1.0: 1998-08-10
  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: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description