7OVU | pdb_00007ovu

Crystal structure of Arabidopsis thaliana NAT9 in complex with AcCoA

PDB DOI: https://doi.org/10.2210/pdb7OVU/pdb

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

Deposited: 2021-06-15 Released: 2022-12-21
Deposition Author(s): Layer, D., Weyer, F.A., 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:
0.181 (Depositor), 0.180 (DCC)
R-Value Work:
0.149 (Depositor), 0.150 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of the Arabidopsis thaliana N-acetyltransferase 9

Layer, D., Weyer, F.A., Kopp, J., Sinning, I.

To be published.

Macromolecule Content

Total Structure Weight: 25.37 kDa
Atom Count: 1,801
Modeled Residue Count: 196
Deposited Residue Count: 218
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA N-acyltransferases (NAT) superfamily protein	A	218	Arabidopsis thaliana	Mutation(s): 0 Gene Names: At2g04845 EC: 2.3.1.48
UniProt
Find proteins for Q8S8E7 (Arabidopsis thaliana) Explore Q8S8E7 Go to UniProtKB: Q8S8E7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8S8E7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO (Subject of Investigation/LOI) Query on ACO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.181 (Depositor), 0.180 (DCC)
R-Value Work: 0.149 (Depositor), 0.150 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.202	α = 90
b = 48.895	β = 102.75
c = 60.123	γ = 90

Software Package:

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