5ZY9 | pdb_00005zy9

Structural basis for a tRNA synthetase

• PDB DOI: https://doi.org/10.2210/pdb5ZY9/pdb

• Classification: LIGASE
• Organism(s): Phytophthora sojae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-23 Released: 2019-06-12 
• Deposition Author(s): Zhang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.209 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

Structural basis for inhibition of translational functions on a tRNA synthetase

Zhang, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 143.29 kDa 
• Atom Count: 10,154 
• Modeled Residue Count: 1,198 
• Deposited Residue Count: 1,218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Threonyl-tRNA synthase	A [auth C], B [auth D], C [auth E]	406	Phytophthora sojae	Mutation(s): 0  EC: 6.1.1.3
UniProt
Find proteins for G3FIN0 (Phytophthora sojae) Explore G3FIN0  Go to UniProtKB:  G3FIN0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2CR (Subject of Investigation/LOI)	D [auth C], F [auth D], H [auth E]	(1R,2R)-2-[(2S,4E,6E,8R,9S,11R,13S,15S,16S)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxooxacyclooctadeca-4,6-dien-2-yl]cyclopentanecarboxylic acid C28 H43 N O6 OJCKRNPLOZHAOU-RSXXJMTFSA-N
ZN (Subject of Investigation/LOI)	E [auth C], G [auth D], I [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.209 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.220 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.212	α = 90
b = 109.633	β = 99.46
c = 133.766	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Zhang, J.

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description