8XBN | pdb_00008xbn

Crystal structure of Arabidopsis N-amino acetyltransferase NATA1 bound to CoA and HEPES

• PDB DOI: https://doi.org/10.2210/pdb8XBN/pdb

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


• Deposited: 2023-12-06 Released: 2024-12-11 
• Deposition Author(s): Hameed, U.F.S., Arold, S.T.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.184 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Arabidopsis NATA1 bound to CoA and HEPES

Hameed, U.F.S., Arold, S.T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.96 kDa 
• Atom Count: 3,733 
• Modeled Residue Count: 407 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-ornithine N5-acetyltransferase NATA1	A, B [auth C]	215	Arabidopsis thaliana	Mutation(s): 0  Gene Names: NATA1 EC: 2.3.1
UniProt
Find proteins for Q9ZV05 (Arabidopsis thaliana) Explore Q9ZV05  Go to UniProtKB:  Q9ZV05

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA (Subject of Investigation/LOI)	D [auth A], E [auth C]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
EPE (Subject of Investigation/LOI)	C [auth A], F [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.184 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38XBN

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.32	α = 90
b = 76.62	β = 90
c = 82.08	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Hameed, U.F.S., Arold, S.T.

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

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release