2NLM

Crystal structure of the DB 911- D(CGCGAATTCGCG)2 complex at 2.05 A resolution.

• PDB DOI: https://doi.org/10.2210/pdb2NLM/pdb
• NAKB: 2NLM

• Classification: DNA
• Mutation(s): No 


• Deposited: 2006-10-20 Released: 2007-10-30 
• Deposition Author(s): Lee, M.P.H., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.329 
• R-Value Work: 0.256 
• R-Value Observed: 0.256 

Starting Model: experimental

Literature

Crystal structure of the DB 911 - D(CGCGAATTCGCG)2 complex at 2.05 A resolution.

Lee, M.P.H., Neidle, S.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.71 kDa 
• Atom Count: 559 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DB9	D [auth B]	2-{4'-[AMINO(IMINO)METHYL]BIPHENYL-3-YL}-1H-BENZIMIDAZOLE-6-CARBOXIMIDAMIDE C21 H18 N6 LRMPNDUSMWYCMH-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.329 
• R-Value Work: 0.256 
• R-Value Observed: 0.256 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.726	α = 90
b = 40.065	β = 90
c = 65.556	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
CNS	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Lee, M.P.H., Neidle, S.

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description