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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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BMOClick on this verticalbar to view details

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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BMOClick on this verticalbar to view details

View more in-depth experimental data
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