253D

CRYSTAL STRUCTURE OF THE B-DNA NONAMER D(GCGTACGCG) WITH A NOVEL D[G*(G.C)] BASE-TRIPLET INVOLVING THE MINOR GROOVE

• PDB DOI: https://doi.org/10.2210/pdb253D/pdb
• NAKB: 253D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1996-03-20 Released: 1996-04-15 
• Deposition Author(s): Mooers, B.H.M., Ho, P.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.214 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 

Literature

Crystal Structure of the B-DNA Nonamer d(GCGTACGCG) with a Novel d[G*(G.C)] Base-triplet Involving the Minor Groove

Mooers, B.H.M., Ho, P.S.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2.78 kDa 
• Atom Count: 213 
• Modelled Residue Count: 9 
• Deposited Residue Count: 9 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*GP*TP*AP*CP*GP*CP*G)-3')	A	9	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: 2.20 Å
• R-Value Free: 0.214 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.915	α = 90
b = 38.915	β = 90
c = 33.026	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
XSCANS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-04-15 
Deposition Author(s): Mooers, B.H.M., Ho, P.S.

Revision History  

• Version 1.0: 1996-04-15
  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, Derived calculations