7OVV | pdb_00007ovv

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 (Depositor), 0.190 (DCC)
R-Value Work:
0.155 (Depositor), 0.150 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural insights into the Arabidopsis thaliana thialysine acetyltransferase AtNATA2

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

To be published.

Macromolecule Content

Total Structure Weight: 48.8 kDa
Atom Count: 3,655
Modeled Residue Count: 390
Deposited Residue Count: 400
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9ZV06
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5NG (Subject of Investigation/LOI) Query on 5NG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	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		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.188 (Depositor), 0.190 (DCC)
R-Value Work: 0.155 (Depositor), 0.150 (DCC)
R-Value Observed: 0.157 (Depositor)

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-12-21

Deposition Author(s):

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 (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.