7LU4

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 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

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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.

Macromolecules
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(by identity cutoff)  |  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
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  • 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 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • 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

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Ligand Structure Quality Assessment 


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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