2GWA | pdb_00002gwa

Crystal Structure of a Complex Formed Between the DNA Holliday Junction and a Bis-Acridine Molecule.

• PDB DOI: https://doi.org/10.2210/pdb2GWA/pdb
• NAKB: 2GWA

• Classification: DNA
• Mutation(s): No 


• Deposited: 2006-05-04 Released: 2006-06-06 
• Deposition Author(s): Brogden, A.L., Hopcroft, N.H., Cardin, C.J., Searcey, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.310 (Depositor) 
• R-Value Work: 
  0.268 (Depositor), 0.271 (DCC) 
• R-Value Observed: 
  0.277 (Depositor) 

Starting Model: experimental

Literature

Ligand bridging of the DNA Holliday junction: molecular recognition of a stacked-X four-way junction by a small molecule.

Brogden, A.L., Hopcroft, N.H., Searcey, M., Cardin, C.J.

(2007) Angew Chem Int Ed Engl 46: 3850-3854

• PubMed: 17477457 
• DOI: https://doi.org/10.1002/anie.200603760
• Primary Citation Related Structures: 
  2GWA

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Organizational Affiliation: 
• School of Chemistry, University of Reading, Whiteknights, Reading, Berkshire, RG6 6AD, UK.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.99 kDa 
• Atom Count: 573 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*Tp*Cp*Gp*Gp*Tp*Ap*Cp*Cp*Gp*A)-3'	A, B	10	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A4C	C [auth A]	9,9'-(HEXANE-1,6-DIYLDIIMINO)BIS{N-[2-(DIMETHYLAMINO)ETHYL]ACRIDINE-4-CARBOXAMIDE} C42 H50 N8 O2 ATHNVLFOCKEETH-UHFFFAOYSA-N
SPM	D [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.310 (Depositor) 
• R-Value Work:  0.268 (Depositor), 0.271 (DCC) 
• R-Value Observed: 0.277 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.224	α = 90
b = 25.142	β = 110.97
c = 37.541	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
MAR345	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-06 
Deposition Author(s): Brogden, A.L., Hopcroft, N.H., Cardin, C.J., Searcey, M.

Revision History  

• Version 1.0: 2006-06-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description