5KTV | pdb_00005ktv

Mis-pairing of unnatural base Z-G DNA duplex at pH 8.5

PDB DOI: https://doi.org/10.2210/pdb5KTV/pdb
NAKB: 5KTV

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

Deposited: 2016-07-12 Released: 2017-05-03
Deposition Author(s): Ahmad Sobri, A.F., Brady, R.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.180 (Depositor), 0.190 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural Basis of the Mispairing of an Artificially Expanded Genetic Information System

Reichenbach, L.F., Ahmad Sobri, A.F., Zaccai, N.R., Agnew, C., Burton, N., Eperon, L.P., de Ornellas, S., Eperon, I.C., Brady, R.L., Burley, G.A.

(2017) Chemistry

DOI: https://doi.org/10.1016/j.chempr.2016.11.009

Macromolecule Content

Total Structure Weight: 7.78 kDa
Atom Count: 485
Modeled Residue Count: 22
Deposited Residue Count: 24
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(PGPCPGPAPAPTPTP(1W5)PGPCP*G)-3')	A, B	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.180 (Depositor), 0.190 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.924	α = 90
b = 40.924	β = 90
c = 102.147	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-05-03

Deposition Author(s):

Ahmad Sobri, A.F.

Brady, R.L.

Revision History (Full details and data files)

Version 1.0: 2017-05-03
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description

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