7LU4 | pdb_00007lu4

Crystal structure of bacterial glycyl tRNA synthetase in complex with glycine

• PDB DOI: https://doi.org/10.2210/pdb7LU4/pdb

• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of bacterial glycyl tRNA synthetase in complex with glycine

Torres-Larios, A.

To be published.

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: light scattering

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multifunctional fusion protein	A, B	1,011	Thermanaerothrix daxensis	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLY (Subject of Investigation/LOI)	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), 0.230 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 238.58	α = 90
b = 127.86	β = 103.61
c = 133.06	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MrBUMP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): Torres-Larios, A.

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Funding Organization	Location	Grant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)	Mexico	CB2015-253323
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)	Mexico	IN204820

Revision History  

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