8XJ9 | pdb_00008xj9

Crystal Structure of Arabidopsis N-amino acetyltransferase 2 (AtNATA2)

PDB DOI: https://doi.org/10.2210/pdb8XJ9/pdb

Classification: TRANSFERASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2023-12-21 Released: 2024-12-25
Deposition Author(s): Arold, S.T., Hameed, U.F.S.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.195 (Depositor), 0.198 (DCC)
R-Value Work:
0.153 (Depositor), 0.163 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Arabidopsis N-amino acetyltransferase 2 (AtNATA2)

Arold, S.T., Hameed, U.F.S.

To be published.

Macromolecule Content

Total Structure Weight: 24.33 kDa
Atom Count: 1,841
Modeled Residue Count: 204
Deposited Residue Count: 212
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN5-related N-acetyltransferase 8	A	212	Arabidopsis thaliana	Mutation(s): 0 Gene Names: GNAT8 EC: 2.3.1.48
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE (Subject of Investigation/LOI) Query on PGE 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]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.195 (Depositor), 0.198 (DCC)
R-Value Work: 0.153 (Depositor), 0.163 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.7	α = 90
b = 54.84	β = 113.9
c = 51.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-12-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	Saudi Arabia	KIng Abdullah University of Science and Technology

Revision History (Full details and data files)

Version 1.0: 2024-12-25
Type: Initial release

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.