1EHZ

The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited

Shi, H.Moore, P.B.

(2000) RNA 6: 1091-1105

  • DOI: 10.1017/s1355838200000364
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of the monoclinic form of yeast phenylalanine tRNA has been redetermined at a resolution of 1.93 A. The structure of yeast tRNAphe described here is more accurate than its predecessors not only because it incorporates higher res ...

    The crystal structure of the monoclinic form of yeast phenylalanine tRNA has been redetermined at a resolution of 1.93 A. The structure of yeast tRNAphe described here is more accurate than its predecessors not only because it incorporates higher resolution data, but also because it has been refined using techniques that had not been developed when its predecessors were determined more than 20 years ago. The 1.93 A resolution version of this structure differs interestingly from its predecessors in its details. In loop regions particularly, the backbone torsion angles in the new structure are not the same as those reported earlier. Several new divalent cation binding sites have been identified, and the water structure that has emerged is also different.


    Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
TRANSFER RNA (PHE)A76Saccharomyces cerevisiae
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.981α = 90
b = 33.389β = 90.2
c = 61.921γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2000-02-23 
  • Released Date: 2000-10-02 
  • Deposition Author(s): Shi, H., Moore, P.B.

Revision History 

  • Version 1.0: 2000-10-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2011-12-21
    Changes: Source and taxonomy