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), 0.208 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7EEO

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:

Molecule	Chains	Length	Organism	Image
Entity ID: 1
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), 0.208 (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

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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

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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.