387D | pdb_0000387d

RNA Pseudoknot with 3D Domain Swapping

PDB DOI: https://doi.org/10.2210/pdb387D/pdb
NAKB: 387D

Classification: RNA
Mutation(s): No

Deposited: 1998-04-14 Released: 2003-08-26
Deposition Author(s): Lietzke, S.E., Kundrot, C.E., Barnes, C.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.234 (Depositor)
R-Value Work:
0.181 (Depositor)
R-Value Observed:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The Structure of an RNA Pseudoknot Shows 3D Domain Swapping

Lietzke, S.E., Barnes, C.L., Malone, V.F., Jones, J.T., Kundrot, C.E.

(1998) Structure, Motion, Interaction And Expression Of Biological Macromolecules, The Proceedings Of The Tenth Conversation Held At The University-suny, Albany Ny, June 17-21, 1997 10: 91-101

Macromolecule Content

Total Structure Weight: 8.39 kDa
Atom Count: 562
Modeled Residue Count: 26
Deposited Residue Count: 26
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
RNA Pseudoknot	A	26	N/A
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.234 (Depositor)
R-Value Work: 0.181 (Depositor)
R-Value Observed: 0.181 (Depositor)

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.6	α = 90
b = 61.6	β = 90
c = 98.9	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XSCALE	data scaling
X-PLOR	refinement
XDS	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-08-26

Deposition Author(s):

Lietzke, S.E.

Kundrot, C.E.

Barnes, C.L.

Revision History (Full details and data files)

Version 1.0: 2003-08-26
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-04-04
Changes: Data collection
Version 1.4: 2023-12-27
Changes: Data collection, Database references

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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.