7OVV

Crystal structure of the Arabidopsis thaliana thialysine acetyltransferase AtNATA2

• PDB DOI: https://doi.org/10.2210/pdb7OVV/pdb

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-06-15 Released: 2022-12-21 
• Deposition Author(s): Layer, D., Kopp, J., Sinning, I.
• Funding Organization(s): German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.188 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 

Starting Model: experimental

Literature

Structural insights into the Arabidopsis thaliana thialysine acetyltransferase AtNATA2

Layer, D., Stier, G., Kopp, J., Sinning, I.

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: 48.8 kDa 
• Atom Count: 3,655 
• Modelled Residue Count: 390 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable acetyltransferase NATA1-like	A, B	200	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At2g39020, T7F6.19 EC: 2.3.1 (PDB Primary Data), 2.3.1.48 (UniProt)
UniProt
Find proteins for Q9ZV06 (Arabidopsis thaliana) Explore Q9ZV06  Go to UniProtKB:  Q9ZV06

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5NG (Subject of Investigation/LOI)	C [auth A], D [auth B]	[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyldisulfanyl]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate C42 H70 N14 O32 P6 S2 YAISMNQCMHVVLO-BJLFRJKCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.188 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.766	α = 90
b = 104.388	β = 108.04
c = 51.786	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-21 
Deposition Author(s): Layer, D., Kopp, J., Sinning, I.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB 1036 (TP22)
German Research Foundation (DFG)	Germany	Leibniz program (SI 586/6-1)

Revision History  

• Version 1.0: 2022-12-21
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description