9K8O | pdb_00009k8o

Crystal structure of a short zinc-dependent DNAzyme minGAA

PDB DOI: https://doi.org/10.2210/pdb9K8O/pdb
NAKB: 9K8O

Classification: DNA-RNA HYBRID
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2024-10-24 Released: 2025-10-29
Deposition Author(s): Yamasaki, K., Yamasaki, T., Kubota, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free:
0.297 (Depositor), 0.294 (DCC)
R-Value Work:
0.205 (Depositor), 0.207 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A minimal Zn2+-dependent RNA-cleaving DNAzyme and its B-DNA-like crystal and solution structures

Yamasaki, K., Inomata, R., Yamasaki, T., Kubota, T., Miyashita, N., Takeuchi, K., Miyagishi, M.

To be published.

Macromolecule Content

Total Structure Weight: 26.1 kDa
Atom Count: 1,685
Modeled Residue Count: 83
Deposited Residue Count: 84
Unique nucleic acid chains: 1
Unique hybrid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNAzyme minGAA, catalytic strand	A, C, E, G	10	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
substrate strand for DNAzyme minGAA	B, D, F, H	11	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth D] SDF format, chain K [auth F] MOL2 format, chain I [auth B] MOL2 format, chain J [auth D] MOL2 format, chain K [auth F] mmCIF format, chain I [auth B] mmCIF format, chain J [auth D] mmCIF format, chain K [auth F]	I [auth B], J [auth D], K [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth D] Focus chain K [auth F] Interactions & Density Focus chain I [auth B] Focus chain J [auth D] Focus chain K [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free: 0.297 (Depositor), 0.294 (DCC)
R-Value Work: 0.205 (Depositor), 0.207 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.861	α = 90
b = 81.881	β = 90
c = 81.776	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-10-29
Type: Initial release

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.