6CQ3 | pdb_00006cq3

Crystal structure of DNA dodecamer D(CGCGAATTCGCG)

• PDB DOI: https://doi.org/10.2210/pdb6CQ3/pdb
• NAKB: 6CQ3

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2018-03-14 Released: 2018-05-02 
• Deposition Author(s): Delgado, J.L., Vance, N.R., Kerns, R.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of DNA dodecamer D(CGCGAATTCGCG)

Delgado, J.L., Vance, N.R., Kerns, R.J.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.46 kDa 
• Atom Count: 663 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')	A, B	12	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	E [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
MG	C [auth A], D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.33	α = 90
b = 40.51	β = 90
c = 65.03	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Delgado, J.L., Vance, N.R., Kerns, R.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI08761

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description