4TZZ

Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate and increasing PEG3350 concentration from 20% to 45% post crystallization


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.64 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1016/j.str.2014.07.011
  • Primary Citation of Related Structures:  
    4TZV, 4TZW, 4TZX, 4TZY, 4TZP, 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 re ...

    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. Electronic address: adrian.ferre@nih.gov.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-associated protein L7Ae-likeADGJ82Bacillus subtilisMutation(s): 0 
Gene Names: rplGBybaBybxFBSU01090
Find proteins for P46350 (Bacillus subtilis (strain 168))
Explore P46350 
Go to UniProtKB:  P46350
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
engineered tRNAGlyB, E, H, K75Bacillus subtilis
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
T-box Stem I RNAC, F, I, L102Oceanobacillus iheyensis
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
B, C, E, F, H, I, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,D,G,JL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.64 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.641α = 90
b = 260.733β = 92.8
c = 70.698γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references