7JLH | pdb_00007jlh

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

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

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): Yatsunyk, L.A., Chen, E.V.

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

Revision History  

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