2GJB | pdb_00002gjb

Crosslinking of DNA duplexes: X-ray crystal structure of an unsubstituted bisacridine with the oligonucleotide d(CGTACG)

• PDB DOI: https://doi.org/10.2210/pdb2GJB/pdb
• NAKB: 2GJB

• Classification: DNA
• Mutation(s): No 


• Deposited: 2006-03-30 Released: 2007-04-10 
• Deposition Author(s): Gan, Y., Cardin, C.J., Denny, W.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.305 (Depositor), 0.334 (DCC) 
• R-Value Work: 
  0.270 (Depositor), 0.263 (DCC) 
• R-Value Observed: 
  0.272 (Depositor) 

Starting Model: experimental

Literature

Crosslinking of DNA duplexes: X-ray crystal structure of an unsubstituted bisacridine with oligonucleotide d(CGTACG)

Gan, Y., Cardin, C.J., Denny, W.A.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.33 kDa 
• Atom Count: 141 
• Modeled Residue Count: 6 
• Deposited Residue Count: 6 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*TP*AP*CP*GP*)-3'	A	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMO	C [auth A]	N-ACRIDIN-9-YL-N'-[3-(ACRIDIN-9-YLAMINO)PROPYL]PROPANE-1,3-DIAMINE C32 H31 N5 WGBHBVVVCBOHMA-UHFFFAOYSA-N
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.305 (Depositor), 0.334 (DCC) 
• R-Value Work:  0.270 (Depositor), 0.263 (DCC) 
• R-Value Observed: 0.272 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.75	α = 90
b = 25.75	β = 90
c = 78.994	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-10 
Deposition Author(s): Gan, Y., Cardin, C.J., Denny, W.A.

Revision History  

• Version 1.0: 2007-04-10
  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: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.5: 2024-04-03
  Changes: Refinement description