7LU4 | pdb_00007lu4

Crystal structure of bacterial glycyl tRNA synthetase in complex with glycine

  • Classification: LIGASE
  • Organism(s): Thermanaerothrix daxensis
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): Yes 

  • Deposited: 2021-02-20 Released: 2021-08-04 
  • Deposition Author(s): Torres-Larios, A.
  • Funding Organization(s): Consejo Nacional de Ciencia y Tecnologia (CONACYT), Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.228 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7LU4

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

Crystal structure of bacterial glycyl tRNA synthetase in complex with glycine

Torres-Larios, A.

To be published.

Macromolecule Content 

  • Total Structure Weight: 227.47 kDa 
  • Atom Count: 14,715 
  • Modeled Residue Count: 1,955 
  • Deposited Residue Count: 2,022 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Multifunctional fusion protein
A, B
1,011Thermanaerothrix daxensisMutation(s): 5 
Gene Names: glyS, glyQ, SE15_09895
EC: 6.1.1.14
UniProt
Find proteins for A0A0P6Y0P9 (Thermanaerothrix daxensis)
Explore A0A0P6Y0P9 
Go to UniProtKB:  A0A0P6Y0P9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0P6Y0P9
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLY
(Subject of Investigation/LOI)

Query on GLY


Download:Ideal Coordinates CCD File
C [auth B]GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.228 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 238.58α = 90
b = 127.86β = 103.61
c = 133.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)MexicoCB2015-253323
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)MexicoIN204820

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description