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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

Grenoble Outstation, European Molecular Biology Laboratory, France.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A8L1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 ?
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 ( ? )	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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.