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:  
    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 ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-associated protein L7Ae-likeA, D, G, J82Bacillus subtilisMutation(s): 0 
Gene Names: rplGB, ybaB, ybxF, BSU01090
UniProt
Find proteins for P46350 (Bacillus subtilis (strain 168))
Explore P46350 
Go to UniProtKB:  P46350
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46350
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
engineered tRNAGlyB, E, H, K 75Bacillus subtilis
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
T-box Stem I RNAC, F, I, L 102Oceanobacillus iheyensis
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth F],
BA [auth F],
CA [auth F],
DA [auth H],
EA [auth H],
AA [auth F],
BA [auth F],
CA [auth F],
DA [auth H],
EA [auth H],
FA [auth H],
GA [auth H],
HA [auth H],
IA [auth I],
JA [auth I],
KA [auth I],
LA [auth I],
M [auth B],
MA [auth I],
N [auth B],
NA [auth L],
O [auth C],
OA [auth L],
P [auth C],
Q [auth C],
R [auth C],
S [auth E],
T [auth E],
U [auth E],
V [auth E],
W [auth E],
X [auth E],
Y [auth E],
Z [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, D, G, J L-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  (Full details and data files)

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