3GVN

The 1.2 Angstroem crystal structure of an E.coli tRNASer acceptor stem microhelix reveals two magnesium binding sites


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


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Literature

The 1.2A crystal structure of an E. coli tRNASer)acceptor stem microhelix reveals two magnesium binding sites.

Eichert, A.Furste, J.P.Schreiber, A.Perbandt, M.Betzel, C.Erdmann, V.A.Forster, C.

(2009) Biochem.Biophys.Res.Commun. 386: 368-373

  • DOI: 10.1016/j.bbrc.2009.06.048

  • PubMed Abstract: 
  • tRNA identity elements assure the correct aminoacylation of tRNAs by the cognate aminoacyl-tRNA synthetases. tRNA(Ser) belongs to the so-called class II system, in which the identity elements are rather simple and are mostly located in the acceptor s ...

    tRNA identity elements assure the correct aminoacylation of tRNAs by the cognate aminoacyl-tRNA synthetases. tRNA(Ser) belongs to the so-called class II system, in which the identity elements are rather simple and are mostly located in the acceptor stem region, in contrast to 'class I', where tRNA determinants are more complex and are located within different regions of the tRNA. The structure of an Escherichia coli tRNA(Ser) acceptor stem microhelix was solved by high resolution X-ray structure analysis. The RNA crystallizes in the space group C2, with one molecule per asymmetric unit and with the cell constants a=35.79, b=39.13, c=31.37A, and beta=111.1 degrees . A defined hydration pattern of 97 water molecules surrounds the tRNA(Ser) acceptor stem microhelix. Additionally, two magnesium binding sites were detected in the tRNA(Ser) aminoacyl stem.


    Organizational Affiliation

    Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*GP*GP*UP*GP*AP*GP*G)-3'A7N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*CP*CP*UP*CP*AP*CP*C)-3'B7N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 35.793α = 90.00
b = 39.126β = 111.08
c = 31.367γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance