7EEO | pdb_00007eeo

Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA

PDB DOI: https://doi.org/10.2210/pdb7EEO/pdb
NAKB: 7EEO

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

Deposited: 2021-03-19 Released: 2022-03-23
Deposition Author(s): Kondo, J., Sekiguchi, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.265 (Depositor), 0.270 (DCC)
R-Value Work:
0.207 (Depositor), 0.210 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA

Kondo, J., Sekiguchi, S.

To be published.

Macromolecule Content

Total Structure Weight: 18.18 kDa
Atom Count: 1,052
Modeled Residue Count: 47
Deposited Residue Count: 54
Unique hybrid chains: 1

Macromolecules

Find similar nucleic acids by: | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA/RNA (27-MER)	A, B	27	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NCO Query on NCO 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]	COBALT HEXAMMINE(III) Co H₁₈ N₆ DYLMFCCYOUSRTK-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: 2.70 Å
R-Value Free: 0.265 (Depositor), 0.270 (DCC)
R-Value Work: 0.207 (Depositor), 0.210 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.776	α = 90
b = 116.432	β = 107.22
c = 27.904	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2022-03-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-03-23
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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.