4TZX | pdb_00004tzx

Vibrio Vulnificus Adenine Riboswitch variant, grown in Mg2+

• PDB DOI: https://doi.org/10.2210/pdb4TZX/pdb
• NAKB: 4TZX

• Classification: RNA
• Organism(s): Vibrio vulnificus
• Mutation(s): No 


• Deposited: 2014-07-11 Released: 2014-09-10 
• Deposition Author(s): Zhang, J., Ferre-D'Amare, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.257 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

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

• PubMed: 25185828 
• DOI: https://doi.org/10.1016/j.str.2014.07.011
• Primary Citation 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.

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Organizational Affiliation: 
• National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA.
National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA. Electronic address: [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.04 kDa 
• Atom Count: 1,632 
• Modeled Residue Count: 71 
• Deposited Residue Count: 71 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Vibrio vulnificus Adenine Riboswitch	A [auth X]	71	Vibrio vulnificus

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE	B [auth X]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N
MG	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 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.641	α = 90
b = 152.839	β = 90
c = 24.991	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-10 
Deposition Author(s): Zhang, J., Ferre-D'Amare, A.R.

Revision History  

• 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