8I9I | pdb_00008i9i

Glutamyl-tRNA synthetase from Escherichia Coli bound to Glutamate and Zinc

• PDB DOI: https://doi.org/10.2210/pdb8I9I/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-02-07 Released: 2023-04-19 
• Deposition Author(s): Dev, A., Chongdar, N., Dasgupta, S., Basu, G.
• Funding Organization(s): Department of Science & Technology (DST, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.296 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Starting Model: experimental

Literature

Escherichia coli GluRS

Dev, A., Chongdar, N., Dasgupta, S., Basu, G.

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 107.35 kDa 
• Atom Count: 7,513 
• Modeled Residue Count: 935 
• Deposited Residue Count: 936 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate--tRNA ligase	A, B	468	Escherichia coli	Mutation(s): 2  Gene Names: gltX EC: 6.1.1.17
UniProt
Find proteins for P04805 (Escherichia coli (strain K12)) Explore P04805  Go to UniProtKB:  P04805

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLU (Subject of Investigation/LOI)	C [auth A], E [auth B]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
ZN (Subject of Investigation/LOI)	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.296 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 211.51	α = 90
b = 61.29	β = 96.69
c = 101.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-19 
Deposition Author(s): Dev, A., Chongdar, N., Dasgupta, S., Basu, G.

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Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	--

Revision History  

• Version 1.0: 2023-04-19
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection