2I5A | pdb_00002i5a

Crystal structure of a DB1055-D(CGCGAATTCGCG)2 complex

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2006-08-24 Released: 2008-04-08 
  • Deposition Author(s): Neidle, S., Lee, M.P.H.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.287 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Crystal structure of a DB1055-D(CGCGAATTCGCG)2 complex

Neidle, S., Lee, M.P.H.

To be published.

Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
A, B
12N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M1B
Query on M1B
Download Ideal Coordinates CCD File 
D [auth A]2-{3'-[AMINO(IMINO)METHYL]BIPHENYL-4-YL}-1H-BENZIMIDAZOLE-5-CARBOXIMIDAMIDE
C21 H18 N6
JTEAXLWMBHFLPI-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.287 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.145α = 90
b = 39.842β = 90
c = 65.794γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
CNSrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

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: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-31
    Changes: Experimental preparation
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description