1SRY | pdb_00001sry

REFINED CRYSTAL STRUCTURE OF THE SERYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1SRY/pdb

• Classification: LIGASE(SYNTHETASE)
• Organism(s): Thermus thermophilus
• Mutation(s): No 


• Deposited: 1993-08-10 Released: 1994-01-31 
• Deposition Author(s): Fujinaga, M., Berthet-Colominas, C., Cusack, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 
  0.184 (Depositor) 

Literature

Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5 A resolution.

Fujinaga, M., Berthet-Colominas, C., Yaremchuk, A.D., Tukalo, M.A., Cusack, S.

(1993) J Mol Biology 234: 222-233

• PubMed: 8230201 
• DOI: https://doi.org/10.1006/jmbi.1993.1576
• Primary Citation Related Structures: 
  1SRY


• PubMed Abstract: 
  

  The three-dimensional structure of the seryl-tRNA synthetase from Thermus thermophilus has been determined and refined at 2.5 A resolution. The final model consists of a dimer of 421 residues each and 190 water molecules. The R-factor is 18.4% for all the data between 10 and 2.5 A resolution. The structure is very similar to that of the homologous enzyme from Escherichia coli, with an r.m.s. difference of 1.5 A for the 357 alpha-carbon atoms considered equivalent. The comparison of the two structures indicates increased hydrophobicity, reduced conformational entropy and reduced torsional strain as possible mechanisms by which thermostability is obtained in the enzyme from the thermophile.

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Organizational Affiliation: 
• EMBL Grenoble Outstation, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 95.76 kDa 
• Atom Count: 6,936 
• Modeled Residue Count: 842 
• Deposited Residue Count: 842 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERYL-tRNA SYNTHETASE	A, B	421	Thermus thermophilus	Mutation(s): 0  EC: 6.1.1.11
UniProt
Find proteins for P34945 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P34945  Go to UniProtKB:  P34945

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work:  0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.03	α = 90
b = 127.46	β = 108.9
c = 63.37	γ = 90

Software Package:

Software Name	Purpose
GROMOS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Fujinaga, M., Berthet-Colominas, C., Cusack, S.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Other