427D | pdb_0000427d

5'-D(*CP*GP*CP*(CH2-DM1)GP*CP*G)-3'

• PDB DOI: https://doi.org/10.2210/pdb427D/pdb
• NAKB: 427D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1998-09-21 Released: 2000-01-24 
• Deposition Author(s): Schuerman, G., Van Meervelt, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Work: 
  0.170 (DCC) 
• R-Value Observed: 
  0.101 (Depositor) 

Starting Model: experimental

Literature

Conformational Flexibility of the DNA Backbone.

Schuerman, G., Van Meervelt, L.

(2000) J Am Chem Soc 122: 232-240

• DOI: https://doi.org/10.1021/ja992180m

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.35 kDa 
• Atom Count: 257 
• Modeled Residue Count: 6 
• Deposited Residue Count: 6 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*(G49)P*CP*G)-3')	A	6	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DM1	B [auth A]	DAUNOMYCIN C27 H29 N O10 STQGQHZAVUOBTE-VGBVRHCVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Work:  0.170 (DCC) 
• R-Value Observed: 0.101 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.818	α = 90
b = 27.818	β = 90
c = 51.858	γ = 90

Software Package:

Software Name	Purpose
SHELXL	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-24 
Deposition Author(s): Schuerman, G., Van Meervelt, L.

Revision History  

• Version 1.0: 2000-01-24
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description