2V6W | pdb_00002v6w

tRNASer acceptor stem: Conformation and hydration of a microhelix in a crystal structure at 1.8 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb2V6W/pdb
• NAKB: 2V6W

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


• Deposited: 2007-07-23 Released: 2007-11-06 
• Deposition Author(s): Foerster, C., Brauer, A.B.E., Brode, S., Fuerste, J.P., Betzel, C., Erdmann, V.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 
  0.154 (Depositor), 0.159 (DCC) 

Literature

Trnaser Acceptor Stem: Conformation and Hydration of a Microhelix in a Crystal Structure at 1.8 A Resolution.

Forster, C., Brauer, A.B.E., Brode, S., Furste, J.P., Betzel, C., Erdmann, V.A.

(2007) Acta Crystallogr D Biol Crystallogr 63: 1154

• PubMed: 18007030 
• DOI: https://doi.org/10.1107/S0907444907045271
• Primary Citation Related Structures: 
  2V6W


• PubMed Abstract: 
  

  The crystal structure of a serine-specific tRNA acceptor-stem microhelix, the binding site for the seryl-tRNA synthetase, was solved by X-ray analysis. This seven-base-pair tRNA(Ser) microhelix forms endless rows of helices in the crystal lattice, with two helices stacking 'head-to-head' onto each other, resulting in an intermolecular guanosine stacking of the first purine nucleotides at the 5'-strands of the tRNA(Ser) microhelices. A network of 75 water loci could be associated with each RNA duplex. Unusual local geometric backbone parameters could be detected in the region of the G4 phosphate located in the 5'-strand of the helix, which lead to a ;kink' in this region and to an irregularly bent helix. The role of the specific hydration pattern and of the irregular conformation of the tRNA(Ser) acceptor-stem helix is discussed and summarized.

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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)

Macromolecule Content 

• Total Structure Weight: 4.42 kDa 
• Atom Count: 367 
• 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*AP*GP*AP*GP*AP)-3'	A	7	Escherichia coli

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work:  0.154 (Depositor), 0.159 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.1	α = 90
b = 38.92	β = 110.61
c = 30.79	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Foerster, C., Brauer, A.B.E., Brode, S., Fuerste, J.P., Betzel, C., Erdmann, V.A.

Revision History  

• Version 1.0: 2007-11-06
  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: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Other