5M68 | pdb_00005m68

AT-rich DNA dodecamer with extra helical guanine-nickel coordination

• PDB DOI: https://doi.org/10.2210/pdb5M68/pdb
• NAKB: 5M68

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


• Deposited: 2016-10-24 Released: 2017-11-15 
• Deposition Author(s): Campos, J.L., Saperas, N., Acosta-Reyes, F.J., Pagan, M.
• Funding Organization(s): MINECO - FEDER, Generalitat de Catalunya

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.247 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

AT-rich DNA with extra helical guanine-nickel coordination

Campos, J.L., Saperas, N., Acosta-Reyes, F.J., Pagan, M.

To be published.

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.61 kDa 
• Atom Count: 1,427 
• Modeled Residue Count: 66 
• Deposited Residue Count: 72 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	G [auth A], H [auth A], I [auth B], J [auth C], K [auth C], L [auth D], M [auth D], N [auth E], O [auth E], P [auth F], Q [auth F]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.247 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.78	α = 90
b = 44.78	β = 90
c = 99.01	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Campos, J.L., Saperas, N., Acosta-Reyes, F.J., Pagan, M.

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Funding Organization	Location	Grant Number
MINECO - FEDER	Spain	BFU-2009-10380
Generalitat de Catalunya	Spain	SGR-2009-1208

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Data collection, Source and taxonomy
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations