2VAL

Crystal structure of an Escherichia coli tRNAGly microhelix at 2.0 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb2VAL/pdb
• NAKB: 2VAL

• Classification: RNA
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2007-09-03 Released: 2007-10-16 
• Deposition Author(s): Forster, C., Brauer, A.B.E., Perbandt, M., Lehmann, D., Furste, J.P., Betzel, C., Erdmann, V.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.318 
• R-Value Work: 0.241 

Literature

Crystal Structure of an Escherichia Coli Trnagly Microhelix at 2.0 Angstrom Resolution

Forster, C., Brauer, A.B.E., Perbandt, M., Lehmann, D., Furste, J.P., Betzel, C., Erdmann, V.A.

(2007) Biochem Biophys Res Commun 363: 621

• PubMed: 17888869 
• DOI: https://doi.org/10.1016/j.bbrc.2007.09.008
• Primary Citation of Related Structures:  
  2VAL


• PubMed Abstract: 
  

  tRNA identity elements determine the correct aminoacylation by the cognate aminoacyl-tRNA synthetase. In class II aminoacyl tRNA synthetase systems, tRNA specificity is assured by rather few and simple recognition elements, mostly located in the acceptor stem of the tRNA. Here we present the crystal structure of an Escherichia coli tRNA(Gly) aminoacyl stem microhelix at 2.0 A resolution. The tRNA(Gly) microhelix crystallizes in the space group P3(2)21 with the cell constants a=b=35.35 A, c=130.82 A, gamma=120 degrees . The helical parameters, solvent molecules and a potential magnesium binding site are discussed.

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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 PQS (software)

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 8.89 kDa 
• Atom Count: 643 
• Modelled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*CP*GP*GP*GP*AP*AP)-3'	A, B	7	Escherichia coli

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*UP*UP*CP*CP*CP*GP*CP)-3'	C, D	7	Escherichia coli

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.318 
• R-Value Work: 0.241 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.348	α = 90
b = 35.348	β = 90
c = 130.821	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-16 
Deposition Author(s): Forster, C., Brauer, A.B.E., Perbandt, M., Lehmann, D., Furste, J.P., Betzel, C., Erdmann, V.A.

Revision History  

• Version 1.0: 2007-10-16
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection
• Version 1.4: 2019-10-16
  Changes: Data collection, Other