5I4S | pdb_00005i4s

Non-natural DNA pair Z (6-amino-5-nitro-2[1H] pyridone heterocycle)-Guanosine

• PDB DOI: https://doi.org/10.2210/pdb5I4S/pdb
• NAKB: 5I4S

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


• Deposited: 2016-02-12 Released: 2017-02-22 
• Deposition Author(s): Ahmad Sobri, A.F., Brady, R.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Non-natural DNA pair Z (6-amino-5-nitro-2[1H] pyridone heterocycle)-Guanosine

Ahmad Sobri, A.F., Brady, R.L.

To be published.

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 7.74 kDa 
• Atom Count: 484 
• Modeled Residue Count: 22 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*(D8Z)P*GP*CP*G)-3')	A, B	12	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.487	α = 90
b = 41.487	β = 90
c = 101.738	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-22 
Deposition Author(s): Ahmad Sobri, A.F., Brady, R.L.

Revision History  

• Version 1.0: 2017-02-22
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Source and taxonomy
• Version 1.2: 2019-10-16
  Changes: Data collection
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description