4JRD | pdb_00004jrd

Crystal structure of the parallel double-stranded helix of poly(A) RNA

PDB DOI: https://doi.org/10.2210/pdb4JRD/pdb
NAKB: 4JRD

Classification: RNA
Mutation(s): No

Deposited: 2013-03-21 Released: 2013-06-05
Deposition Author(s): Safaee, N., Noronha, A.M., Kozlov, G., Rodionov, D., Wilds, C.J., Sheldrick, G.M., Gehring, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free:
0.158 (Depositor), 0.155 (DCC)
R-Value Work:
0.118 (Depositor), 0.129 (DCC)
R-Value Observed:
0.126 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of the parallel duplex of poly(A) RNA: evaluation of a 50 year-old prediction.

Safaee, N., Noronha, A.M., Rodionov, D., Kozlov, G., Wilds, C.J., Sheldrick, G.M., Gehring, K.

(2013) Angew Chem Int Ed Engl 52: 10370-10373

PubMed: 23813654 Search on PubMed
DOI: https://doi.org/10.1002/anie.201303461
Primary Citation Related Structures:
4JRD

Organizational Affiliation

Department of Biochemistry, McGill University, Montréal, Québec, H3G 0B1 (Canada); Groupe de recherche axé sur la structure des protéines McGill University, Montréal, Québec, H3G 0B1 (Canada). nozhat.safaee@mail.mcgill.ca.

Macromolecule Content

Total Structure Weight: 7.48 kDa
Atom Count: 572
Modeled Residue Count: 22
Deposited Residue Count: 22
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
RNA (5'-R(APAPAPAPAPAPAPAPAPAP*A)-3')	A, B	11	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.158 (Depositor), 0.155 (DCC)
R-Value Work: 0.118 (Depositor), 0.129 (DCC)
R-Value Observed: 0.126 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 22.8	α = 90
b = 22.8	β = 90
c = 163.7	γ = 90

Software Package:

Software Name	Purpose
MxDC	data collection
SHELXD	phasing
SHELXL	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-06-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-06-05
Type: Initial release
Version 1.1: 2015-08-12
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations