9QMP | pdb_00009qmp

E.coli seryl-tRNA synthetase

• PDB DOI: https://doi.org/10.2210/pdb9QMP/pdb

• Classification: TRANSLATION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-24 Released: 2025-05-14 
• Deposition Author(s): Cusack, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Literature

A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 A.

Cusack, S., Berthet-Colominas, C., Hartlein, M., Nassar, N., Leberman, R.

(1990) Nature 347: 249-255

• PubMed: 2205803 
• DOI: https://doi.org/10.1038/347249a0
• Primary Citation of Related Structures:  
  9QMP


• PubMed Abstract: 
  

  The three-dimensional crystal structure of seryl-transfer RNA synthetase from Escherichia coli, refined at 2.5 A resolution, is described. It has an N-terminal domain that forms an antiparallel alpha helical coiled-coil, stretching 60 A out into the solvent and stabilized by interhelical hydrophobic interactions and an active-site alpha-beta domain based around a seven-stranded antiparallel beta sheet. Unlike the three other known synthetase structures, the enzyme contains no classical nucleotide-binding fold, and is the first representative of a second class of aminoacyl-tRNA synthetase structures.

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Organizational Affiliation: 

Grenoble Outstation, European Molecular Biology Laboratory, 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 48.48 kDa 
• Atom Count: 3,375 
• Modeled Residue Count: 413 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine--tRNA ligase	A	430	Escherichia coli K-12	Mutation(s): 0  Gene Names: serS, b0893, JW0876 EC: 6.1.1.11
UniProt
Find proteins for P0A8L1 (Escherichia coli (strain K12)) Explore P0A8L1  Go to UniProtKB:  P0A8L1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.648	α = 90
b = 90.72	β = 117.746
c = 69.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
MLPHARE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Cusack, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release