7EDW | pdb_00007edw

DNA duplex containing T-T base pairs in complex with Au(III)

PDB DOI: https://doi.org/10.2210/pdb7EDW/pdb
NAKB: 7EDW

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

Deposited: 2021-03-17 Released: 2022-03-23
Deposition Author(s): Kondo, J., Iwase, E.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.186 (Depositor), 0.190 (DCC)
R-Value Work:
0.165 (Depositor), 0.170 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

DNA duplex containing T-T base pairs in complex with Au(III)

Kondo, J., Iwase, E.

To be published.

Macromolecule Content

Total Structure Weight: 7.9 kDa
Atom Count: 543
Modeled Residue Count: 24
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(GPGPAPCPCPTPTPGPGPTPCPC)-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
AU (Subject of Investigation/LOI) Query on AU Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.186 (Depositor), 0.190 (DCC)
R-Value Work: 0.165 (Depositor), 0.170 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.076	α = 90
b = 42.8	β = 90
c = 67.383	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
AutoSol	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-03-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	24245037

Revision History (Full details and data files)

Version 1.0: 2022-03-23
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.