2GJB | pdb_00002gjb

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.305 (Depositor), 0.330 (DCC) 
  • R-Value Work: 
    0.270 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.272 (Depositor) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history. 


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.

Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*CP*GP*TP*AP*CP*GP*)-3'6N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BMO
Query on BMO
Download Ideal Coordinates CCD File 
C [auth A]N-ACRIDIN-9-YL-N'-[3-(ACRIDIN-9-YLAMINO)PROPYL]PROPANE-1,3-DIAMINE
C32 H31 N5
WGBHBVVVCBOHMA-UHFFFAOYSA-N
K
Query on K
Download Ideal Coordinates CCD File 
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), 0.330 (DCC) 
  • R-Value Work:  0.270 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.272 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.75α = 90
b = 25.75β = 90
c = 78.994γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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