3ERS

Crystal Structure of E. coli Trbp111


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Trbp111: a tructure specific tRNA binding protein

Swairjo, M.A.Morales, A.J.Wang, C.-C.Ortiz, A.R.Schimmel, P.

(2000) Embo J. 19: 6287-6298

  • DOI: 10.1093/emboj/19.23.6287
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Trbp111 is a 111 amino acid Aquifex aeolicus structure-specific tRNA-binding protein that has homologous counterparts distributed throughout evolution. A dimer is the functional unit for binding a single tRNA. Here we report the 3D structures of the ...

    Trbp111 is a 111 amino acid Aquifex aeolicus structure-specific tRNA-binding protein that has homologous counterparts distributed throughout evolution. A dimer is the functional unit for binding a single tRNA. Here we report the 3D structures of the A.aeolicus protein and its Escherichia coli homolog at resolutions of 2.50 and 1.87 A, respectively. The structure shows a symmetrical dimer of two core domains and a central dimerization domain where the N- and C-terminal regions of Trbp111 form an extensive dimer interface. The core of the monomer is a classical oligonucleotide/oligosaccharide-binding (OB) fold with a five-stranded ss-barrel and a small capping helix. This structure is similar to that seen in the anticodon-binding domain of three class II tRNA synthetases and several other proteins. Mutational analysis identified sites important for interactions with tRNA. These residues line the inner surfaces of two clefts formed between the ss-barrel of each monomer and the dimer interface. The results are consistent with a proposed model for asymmetrical docking of the convex side of tRNA to the dimer.


    Organizational Affiliation

    Skaags Institute for Chemical Biology, Department of Molecular Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA-binding protein ygjH
X
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ygjH
Find proteins for P42589 (Escherichia coli (strain K12))
Go to UniProtKB:  P42589
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.216 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 41.234α = 90.00
b = 41.234β = 90.00
c = 95.377γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SOLOMONphasing
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-10-03 
  • Released Date: 2008-12-02 
  • Deposition Author(s): Swairjo, M.A.
  • This entry supersedes: 1PXF

Revision History 

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description