Biological Assembly 1  

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Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25335.51 
• Atom Count: 1676 
• Residue Count: 76 
• Unique nucleic acid chains: 1

1EVV

CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTION

• DOI: 10.2210/pdb1EVV/pdb
• NDB: TR0002

• Classification: RNA
• Organism(s): Saccharomyces


• Deposited: 2000-04-20 Released: 2000-05-01 
• Deposition Author(s): Jovine, L., Djordjevic, S., Rhodes, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.263 
• R-Value Work: 0.227 

Literature

The crystal structure of yeast phenylalanine tRNA at 2.0 A resolution: cleavage by Mg(2+) in 15-year old crystals.

Jovine, L., Djordjevic, S., Rhodes, D.

(2000) J.Mol.Biol. 301: 401-414

• PubMed: 10926517 
• DOI: 10.1006/jmbi.2000.3950


• PubMed Abstract: 
  

We have re-determined the crystal structure of yeast tRNA(Phe) to 2. 0 A resolution using 15 year old crystals. The accuracy of the new structure, due both to higher resolution data and formerly unavailable refinement methods, consolidates the previous structural information, but also reveals novel details. In particular, the water structure around the tightly bound Mg(2+) is now clearly resolved, and hence provides more accurate information on the geometry of the magnesium-binding sites and the role of water molecules in coordinating the metal ions to the tRNA. We have assigned a total of ten magnesium ions and identified a partly conserved geometry for high-affinity Mg(2+ )binding. In the electron density map there is also clear density for a spermine molecule binding in the major groove of the TPsiC arm and also contacting a symmetry-related tRNA molecule. Interestingly, we have also found that two specific regions of the tRNA in the crystals are partially cleaved. The sites of hydrolysis are within the D and anticodon loops in the vicinity of Mg(2+).

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Related Citations: 

• Further refinement of the structure of yeast tRNA Phe
  Hingerty, B.,Brown, R.S.,Jack, A.
  (1978) J.Mol.Biol. 124: 523
• Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles
  Westhof, E.,Sundaralingam, M.
  (1986) Biochemistry 25: 4868
• Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals
  Westhof, E.,Dumas, P.,Moras, D.
  (1988) Acta Crystallogr.,Sect.A 44: 112
• High-resolution X-ray diffraction studies on a pure species of transfer RNA
  Ladner, J.E.,Finch, J.T.,Klug, A.,Clark, B.F.
  (1972) J.Mol.Biol. 72: 99
• Structure of yeast phenylalanine tRNA at 3 A resolution
  Robertus, J.D.,Ladner, J.E.,Finch, J.T.,Rhodes, D.,Brown, R.S.,Clark, B.F.C.,Klug, A.
  (1974) Nature 250: 546
• Structure of yeast phenylalanine transfer RNA at 2.5 A resolution
  Ladner, J.E.,Jack, A.,Robertus, J.D.,Brown, R.S.,Rhodes, D.,Clark, B.F.,Klug, A.
  (1975) Proc.Natl.Acad.Sci.USA 72: 4414




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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
PHENYLALANINE TRANSFER RNA	A	76	Saccharomyces

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SPM	A	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  11 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PSU	A	RNA LINKING	C9 H13 N2 O9 P		U
5MC	A	RNA LINKING	C10 H16 N3 O8 P		C
M2G	A	RNA LINKING	C12 H18 N5 O8 P		G
1MA	A	RNA LINKING	C11 H16 N5 O7 P		A
OMC	A	RNA LINKING	C10 H16 N3 O8 P		C
2MG	A	RNA LINKING	C11 H16 N5 O8 P		G
OMG	A	RNA LINKING	C11 H16 N5 O8 P		G
7MG	A	RNA LINKING	C11 H18 N5 O8 P		G
YG	A	RNA LINKING	C21 H29 N6 O12 P		G
5MU	A	RNA LINKING	C10 H15 N2 O9 P		U
H2U	A	RNA LINKING	C9 H15 N2 O9 P		U

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.263 
• R-Value Work: 0.227 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 55.252	α = 90.00
b = 32.988	β = 90.38
c = 61.882	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-04-20 
• Released Date: 2000-05-01 
• Deposition Author(s): Jovine, L., Djordjevic, S., Rhodes, D.

Revision History 

• Version 1.0: 2000-05-01
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance