8V5J | pdb_00008v5j

The Native DNA 16-mer Sequence 5'-GCTGGATTAATCCAGC-3

• PDB DOI: https://doi.org/10.2210/pdb8V5J/pdb
• NAKB: 8V5J

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


• Deposited: 2023-11-30 Released: 2024-12-04 
• Deposition Author(s): Terrell, J.R., Wilson, W.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 
  0.210 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Structural Examination of DNA Minor Groove Binding by Diamidine Stacked Dimers

Terrell, J.R., Paul, A., Ogbonna, E.N., Farahat, A.A., Wilson, W.D.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 5.26 kDa 
• Atom Count: 438 
• Modeled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*GP*GP*AP*TP*TP*AP*AP*TP*CP*CP*AP*GP*C)-3')	A	16	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free:  0.210 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.829	α = 90
b = 38.829	β = 90
c = 159.676	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Terrell, J.R., Wilson, W.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM111749

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release