8PJL | pdb_00008pjl

DNA duplex forming base triplets in minor groove

• PDB DOI: https://doi.org/10.2210/pdb8PJL/pdb
• NAKB: 8PJL

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


• Deposited: 2023-06-23 Released: 2024-07-10 
• Deposition Author(s): Abdullrahman, A., Cardin, C.J., Hall, J.P.
• Funding Organization(s): H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

DNA duplex with triplets bases in minor groove

Abdullrahman, A., Cardin, C.J., Hall, J.P.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 8.74 kDa 
• Atom Count: 693 
• Modeled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*CP*GP*TP*CP*TP*CP*TP*CP*AP*GP*TP*C)-3')	A	14	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*CP*TP*GP*AP*GP*AP*GP*AP*CP*GP*TP*A)-3')	B	14	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	F [auth A], G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.833	α = 90
b = 39.833	β = 90
c = 58.964	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
Aimless	data scaling
SHELXDE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Abdullrahman, A., Cardin, C.J., Hall, J.P.

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Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	H2020-MSCA-ITN-2019-861381

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release