4TZX

Vibrio Vulnificus Adenine Riboswitch variant, grown in Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration.

Zhang, J.Ferre-D'Amare, A.R.

(2014) Structure 22: 1363-1371

  • DOI: https://doi.org/10.1016/j.str.2014.07.011
  • Primary Citation of Related Structures:  
    4TZP, 4TZV, 4TZW, 4TZX, 4TZY, 4TZZ

  • PubMed Abstract: 

    Compared to globular proteins, RNAs with complex 3D folds are characterized by poorly differentiated molecular surfaces dominated by backbone phosphates, sparse tertiary contacts stabilizing global architecture, and conformational flexibility. The resulting generally poor order of crystals of large RNAs and their complexes frequently hampers crystallographic structure determination. We describe and rationalize a postcrystallization treatment strategy that exploits the importance of solvation and counterions for RNA folding. Replacement of Li(+) and Mg(2+) needed for growth of crystals of a tRNA-riboswitch-protein complex with Sr(2+), coupled with dehydration, dramatically improved the resolution limit (8.5-3.2 Å) and data quality, enabling structure determination. The soft Sr(2+) ion forms numerous stabilizing intermolecular contacts. Comparison of pre- and posttreatment structures reveals how RNA assemblies redistribute as quasi-rigid bodies to yield improved crystal packing. Cation exchange complements previously reported postcrystallization dehydration of protein crystals and represents a potentially general strategy for improving crystals of large RNAs.


  • Organizational Affiliation

    National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
Vibrio vulnificus Adenine RiboswitchA [auth X]71Vibrio vulnificus
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADE
Query on ADE

Download Ideal Coordinates CCD File 
B [auth X]ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth X]
D [auth X]
E [auth X]
F [auth X]
G [auth X]
C [auth X],
D [auth X],
E [auth X],
F [auth X],
G [auth X],
H [auth X],
I [auth X],
J [auth X],
K [auth X]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.641α = 90
b = 152.839β = 90
c = 24.991γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy