3GVN | pdb_00003gvn

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

• PDB DOI: https://doi.org/10.2210/pdb3GVN/pdb
• NAKB: 3GVN

• Classification: RNA
• Mutation(s): No 


• Deposited: 2009-03-31 Released: 2009-07-28 
• Deposition Author(s): Eichert, A., Furste, J.P., Schreiber, A., Perbandt, M., Betzel, C., Erdmann, V.A., Forster, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.201 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.193 (DCC) 

Starting Model: experimental

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

• PubMed: 19527687 
• DOI: https://doi.org/10.1016/j.bbrc.2009.06.048
• Primary Citation Related Structures: 
  3GVN


• 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 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.

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Organizational Affiliation: 
• Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 4.48 kDa 
• Atom Count: 392 
• Modeled Residue Count: 14 
• Deposited Residue Count: 14 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*UP*GP*AP*GP*G)-3'	A	7	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*CP*CP*UP*CP*AP*CP*C)-3'	B	7	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.201 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.193 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.793	α = 90
b = 39.126	β = 111.08
c = 31.367	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Eichert, A., Furste, J.P., Schreiber, A., Perbandt, M., Betzel, C., Erdmann, V.A., Forster, C.

Revision History  

• Version 1.0: 2009-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description