8XJ5 | pdb_00008xj5

Crystal structure of AtNATA1 bound to Ornithine and CoA

• PDB DOI: https://doi.org/10.2210/pdb8XJ5/pdb

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


• Deposited: 2023-12-20 Released: 2024-12-25 
• Deposition Author(s): Arold, S.T., Hameed, U.F.S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.251 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of AtNATA1 bound to Ornithine and CoA

Arold, S.T., Hameed, U.F.S.

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: 48.73 kDa 
• Atom Count: 3,180 
• Modeled Residue Count: 370 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-ornithine N5-acetyltransferase NATA1	A, B [auth Q]	205	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], F [auth Q]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
ORN (Subject of Investigation/LOI)	C [auth A], E [auth Q]	L-ornithine C5 H12 N2 O2 AHLPHDHHMVZTML-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.251 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38XJ5

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.04	α = 90
b = 74.07	β = 90
c = 110.39	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: 2024-12-25 
Deposition Author(s): Arold, S.T., Hameed, U.F.S.

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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: 2024-12-25
  Type: Initial release