7ECM | pdb_00007ecm

RNA duplex containing C-A base pair

PDB DOI: https://doi.org/10.2210/pdb7ECM/pdb
NAKB: 7ECM

Classification: RNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2021-03-12 Released: 2022-03-16
Deposition Author(s): Kondo, J., Tsudura, A.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free:
0.196 (Depositor), 0.194 (DCC)
R-Value Work:
0.157 (Depositor), 0.158 (DCC)
R-Value Observed:
0.161 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7ECM

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

Literature

RNA duplex containing C-A base pair

Kondo, J., Tsudura, A.

To be published.

Macromolecule Content

Total Structure Weight: 16.6 kDa
Atom Count: 1,260
Modeled Residue Count: 48
Deposited Residue Count: 48
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
RNA (5'-R(GPGPGPCPCPCPGPGPAPCPCPC)-3')	A, B, C, D	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BA Query on BA Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth C] E [auth A], F [auth A], G [auth A], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D], M [auth D]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free: 0.196 (Depositor), 0.194 (DCC)
R-Value Work: 0.157 (Depositor), 0.158 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.475	α = 100.08
b = 27.909	β = 93.54
c = 46.665	γ = 110.47

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	24245037

Revision History (Full details and data files)

Version 1.0: 2022-03-16
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.