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), 0.185 (DCC)
R-Value Work:
0.149 (Depositor), 0.151 (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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.185 (DCC)
R-Value Work: 0.149 (Depositor), 0.151 (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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.