4AGZ | pdb_00004agz

CRYSTAL STRUCTURE OF THE DB 985-D(CGCGAATTCGCG)2 COMPLEX AT 1.25 A RESOLUTION.

• PDB DOI: https://doi.org/10.2210/pdb4AGZ/pdb
• NAKB: 4AGZ

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2012-02-02 Released: 2013-01-16 
• Deposition Author(s): Munnur, D.G., Mitchell, E.P., Forsyth, V.T., Teixeira, S.C.M., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.207 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.155 (Depositor) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

A Detailed Study of Water Network in the Minor Groove of D(Cgcgaattcgcg)2 and D(Cgcaaatttgcg)2 in Presence of Linear Groove Binders

Munnur, D.G., Mitchell, E.P., Forsyth, V.T., Teixeira, S.C.M., Neidle, S.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 7.77 kDa 
• Atom Count: 725 
• Modeled 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*GP)-3'	A, B	12	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D98	E [auth B]	2-(4'-CARBAMIMIDOYL-2'-HYDROXYBIPHENYL-4-YL)-1H-BENZIMIDAZOLE-5-CARBOXIMIDAMIDE C21 H18 N6 O VYJOWVQQJBILOA-UHFFFAOYSA-N
MG	C [auth A], D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.207 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.155 (Depositor) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.026	α = 90
b = 39.905	β = 90
c = 65.784	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-16 
Deposition Author(s): Munnur, D.G., Mitchell, E.P., Forsyth, V.T., Teixeira, S.C.M., Neidle, S.

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2019-01-30
  Changes: Data collection, Experimental preparation
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description