7JLH

Structure of Centromeric Satellite III Non-canonical Duplex

PDB DOI: https://doi.org/10.2210/pdb7JLH/pdb
NAKB: 7JLH

Classification: DNA
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2020-07-29 Released: 2021-08-04
Deposition Author(s): Yatsunyk, L.A., Chen, E.V.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.255
R-Value Work: 0.221
R-Value Observed: 0.224

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of 4-repeat Satellite III Sequence with Non-Canonical Base Interactions

Yatsunyk, L.A., Chen, E.V., Lee, H.

To be published.

Macromolecule Content

Total Structure Weight: 9.35 kDa
Atom Count: 715
Modelled Residue Count: 30
Deposited Residue Count: 30
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA AATGG	A, B, C, D, E A, B, C, D, E, F	5	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B]	H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.255
R-Value Work: 0.221
R-Value Observed: 0.224
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.522	α = 90
b = 40.217	β = 90
c = 55.379	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
pointless	data scaling
Aimless	data scaling
PHASER	phasing
Coot	model building
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-08-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	1R15CA208676-01A1

Revision History (Full details and data files)

Version 1.0: 2021-08-04
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.