4P2B | pdb_00004p2b

Crystal structure of the apo form of the glutaminyl-tRNA synthetase catalytic domain from Toxoplasma gondii.

• PDB DOI: https://doi.org/10.2210/pdb4P2B/pdb

• Classification: LIGASE
• Organism(s): Toxoplasma gondii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-03-03 Released: 2015-03-18 
• Deposition Author(s): van Rooyen, J.M., Belrhali, H., Hakimi, M.A.
• Funding Organization(s): French National Research Agency, Laboratoire d'Excellence ParaFrap, Fondation Innovations en Infectiologie, Outstanding Scientist Research Programme of the Department of Biotechnology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the apo form of the glutaminyl-tRNA synthetase catalytic domain from Toxoplasma gondii.

van Rooyen, J.M., Belrhali, H., Hakimi, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.61 kDa 
• Atom Count: 3,840 
• Modeled Residue Count: 507 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine aminoacyl-tRNA synthetase	A	576	Toxoplasma gondii	Mutation(s): 0  EC: 6.1.1.18
UniProt
Find proteins for B6KTZ0 (Toxoplasma gondii (strain ATCC 50861 / VEG)) Explore B6KTZ0  Go to UniProtKB:  B6KTZ0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.13	α = 90
b = 105.13	β = 90
c = 229.53	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): van Rooyen, J.M., Belrhali, H., Hakimi, M.A.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-12-BSV3-0009-01
Laboratoire d'Excellence ParaFrap	France	ANR-11-LABX-0024
Fondation Innovations en Infectiologie	France	--
Outstanding Scientist Research Programme of the Department of Biotechnology	India	--

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2015-10-07
  Changes: Experimental preparation
• Version 1.2: 2017-10-04
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary