269D | pdb_0000269d

STRUCTURAL STUDIES ON NUCLEIC ACIDS

• PDB DOI: https://doi.org/10.2210/pdb269D/pdb
• NAKB: 269D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1996-07-12 Released: 1996-08-28 
• Deposition Author(s): Partridge, B.L., Salisbury, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Work: 
  0.161 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

Partridge, B.L., Salisbury, S.A.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.8 kDa 
• Atom Count: 616 
• Modeled 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*GP*CP*GP*AP*AP*TP*TP*(5CM)P*GP*CP*G)-3')	A, B	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HT	D [auth B]	2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE C25 H24 N6 O INAAIJLSXJJHOZ-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Work:  0.161 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.032	α = 90
b = 40.369	β = 90
c = 64.953	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement
RIGAKU	data reduction
RIGAKU	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-08-28 
Deposition Author(s): Partridge, B.L., Salisbury, S.A.

Revision History  

• Version 1.0: 1996-08-28
  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: 2012-02-29
  Changes: Other
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations