1EHZ

The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1EHZ/pdb
• NAKB: 1EHZ

• Classification: RNA
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): Yes 


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

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Experimental Data Snapshot

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

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

• PubMed: 10943889 
• DOI: https://doi.org/10.1017/s1355838200000364
• Primary Citation of Related Structures:  
  1EHZ


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.2 kDa 
• Atom Count: 1,821 
• Modelled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
TRANSFER RNA (PHE)	A	76	Saccharomyces cerevisiae

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A], E [auth A], J [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	B [auth A], D [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 54.981	α = 90
b = 33.389	β = 90.2
c = 61.921	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.4: 2022-12-21
  Changes: Database references, Derived calculations