1M69 | pdb_00001m69

Atomic Resolution Structure of 5Br-9amino-DACA with d[CGTACG]2

• PDB DOI: https://doi.org/10.2210/pdb1M69/pdb
• NAKB: 1M69

• Classification: DNA
• Mutation(s): No 


• Deposited: 2002-07-15 Released: 2003-08-19 
• Deposition Author(s): Teixeira, S.C.M., Thorpe, J.H., Todd, A.K., Cardin, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.186 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Starting Model: experimental

Literature

Heavy Going: the Atomic Resolution Structure of a Topoisomerase II Poison Intercalating into DNA in Multiple Orientations Also Reveals a Multiple Adenine-Thymine Hydrogen Bonding Pattern

Teixeira, S.C.M., Thorpe, J.H., Todd, A.K., Cardin, C.J.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.79 kDa 
• Atom Count: 256 
• 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*G)-3'	A	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DAX	B [auth A], C [auth A]	5-BROMO-N[2-(DIMETHYLAMINO)ETHYL]-9-AMINOACRIDINE-4-CARBOXAMIDE C18 H21 Br N4 O NROQPXQSDDINMC-UHFFFAOYSA-P
SPM	D [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.186 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.186	α = 90
b = 30.186	β = 90
c = 39.443	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
XDS	data reduction
SHELX	model building
SHELXL-97	refinement
XDS	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-19 
Deposition Author(s): Teixeira, S.C.M., Thorpe, J.H., Todd, A.K., Cardin, C.J.

Revision History  

• Version 1.0: 2003-08-19
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-02-08
  Changes: Derived calculations
• Version 1.4: 2017-10-11
  Changes: Refinement description
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.6: 2024-04-03
  Changes: Refinement description