6Y0T | pdb_00006y0t

Sarcin Ricin Loop, mutant C2666A U2653G C2667A

PDB DOI: https://doi.org/10.2210/pdb6Y0T/pdb
NAKB: 6Y0T

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

Deposited: 2020-02-10 Released: 2021-02-17
Deposition Author(s): Ennifar, E., Westhof, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free:
0.203 (Depositor), 0.200 (DCC)
R-Value Work:
0.166 (Depositor), 0.160 (DCC)
R-Value Observed:
0.168 (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

Sarcin Ricin Loop, mutant C2666A U2653G C2667A

Ennifar, E., Westhof, E.

To be published.

Macromolecule Content

Total Structure Weight: 17.96 kDa
Atom Count: 1,583
Modeled Residue Count: 54
Deposited Residue Count: 54
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	C [auth A], D [auth A], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.203 (Depositor), 0.200 (DCC)
R-Value Work: 0.166 (Depositor), 0.160 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.17	α = 90
b = 23.96	β = 108.74
c = 63.82	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-02-17

Deposition Author(s):

Ennifar, E.

Westhof, E.

Revision History (Full details and data files)

Version 1.0: 2021-02-17
Type: Initial release
Version 1.1: 2024-01-24
Changes: Advisory, Data collection, Database references, Refinement description