1SER | pdb_00001ser

THE 2.9 ANGSTROMS CRYSTAL STRUCTURE OF T. THERMOPHILUS SERYL-TRNA SYNTHETASE COMPLEXED WITH TRNA SER

• PDB DOI: https://doi.org/10.2210/pdb1SER/pdb
• NAKB: 1SER

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


• Deposited: 1994-02-21 Released: 1994-04-30 
• Deposition Author(s): Biou, S., Cusack, V., Yaremchuk, A., Tukalo, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser).

Biou, V., Yaremchuk, A., Tukalo, M., Cusack, S.

(1994) Science 263: 1404-1410

• PubMed: 8128220 
• DOI: https://doi.org/10.1126/science.8128220
• Primary Citation of Related Structures:  
  1SER


• PubMed Abstract: 
  

  The crystal structure of Thermus thermophilus seryl-transfer RNA synthetase, a class 2 aminoacyl-tRNA synthetase, complexed with a single tRNA(Ser) molecule was solved at 2.9 A resolution. The structure revealed how insertion of conserved base G20b from the D loop into the core of the tRNA determines the orientation of the long variable arm, which is a characteristic feature of most serine specific tRNAs. On tRNA binding, the antiparallel coiled-coil domain of one subunit of the synthetase makes contacts with the variable arm and T psi C loop of the tRNA and directs the acceptor stem of the tRNA into the active site of the other subunit. Specificity depends principally on recognition of the shape of tRNA(Ser) through backbone contacts and secondarily on sequence specific interactions.

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Organizational Affiliation: 

European Molecular Biology Laboratory, 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.

Macromolecule Content

• Total Structure Weight: 126.14 kDa 
• Atom Count: 7,780 
• Modelled Residue Count: 858 
• Deposited Residue Count: 936 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SERYL-TRNA SYNTHETASE (E.C.6.1.1.11))	B [auth A], C [auth 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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
TRNASER	A [auth T]	94	Thermus thermophilus

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.5	α = 90
b = 128.9	β = 90
c = 121.2	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-04-30 
Deposition Author(s): Biou, S., Cusack, V., Yaremchuk, A., Tukalo, M.

Revision History  

• Version 1.0: 1994-04-30
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Advisory, Derived calculations
• Version 1.4: 2024-02-14
  Changes: Advisory, Data collection, Database references, Derived calculations