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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free:
0.247 (Depositor), 0.270 (DCC)
R-Value Work:
0.227 (Depositor), 0.240 (DCC)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

AT-rich DNA with extra helical guanine-nickel coordination

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

To be published.

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

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(CPGPAPAPTPTPAPAPTPTPCPG)-3')	A, B, C, D, E A, B, C, D, E, F	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth E] SDF format, chain O [auth E] SDF format, chain P [auth F] SDF format, chain Q [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth E] mmCIF format, chain O [auth E] mmCIF format, chain P [auth F] mmCIF format, chain Q [auth F]	G [auth A] H [auth A] I [auth B] J [auth C] K [auth C] 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		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.247 (Depositor), 0.270 (DCC)
R-Value Work: 0.227 (Depositor), 0.240 (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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-11-15

Deposition Author(s):

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

Revision History (Full details and data files)

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