8XJB | pdb_00008xjb

Crystal structure of AtNATA2 bound to Spermine

PDB DOI: https://doi.org/10.2210/pdb8XJB/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: 1.45 Å
R-Value Free:
0.190 (Depositor), 0.198 (DCC)
R-Value Work:
0.151 (Depositor), 0.166 (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 AtNATA2 bound to Spermine

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

To be published.

Macromolecule Content

Total Structure Weight: 24.28 kDa
Atom Count: 1,808
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPM (Subject of Investigation/LOI) Query on SPM 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]	SPERMINE C₁₀ H₂₆ N₄ PFNFFQXMRSDOHW-UHFFFAOYSA-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: 0.190 (Depositor), 0.198 (DCC)
R-Value Work: 0.151 (Depositor), 0.166 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.73	α = 90
b = 54.89	β = 113.64
c = 51.91	γ = 90

Software Package:

Software Name	Purpose
PHENIX	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.