5WY6

Crystal structure of AtNUDX1 (E56A)

• PDB DOI: https://doi.org/10.2210/pdb5WY6/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-01-11 Released: 2017-11-15 
• Deposition Author(s): Liu, J., Guan, Z., Yan, L., Zou, T., Yin, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.213 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Literature

Structural Insights into the Substrate Recognition Mechanism of Arabidopsis GPP-Bound NUDX1 for Noncanonical Monoterpene Biosynthesis.

Liu, J., Guan, Z., Liu, H., Qi, L., Zhang, D., Zou, T., Yin, P.

(2018) Mol Plant 11: 218-221

• PubMed: 29066356 
• DOI: https://doi.org/10.1016/j.molp.2017.10.006
• Primary Citation of Related Structures:  
  5GP0, 5WWD, 5WY6

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Organizational Affiliation: 

National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.65 kDa 
• Atom Count: 2,409 
• Modelled Residue Count: 277 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nudix hydrolase 1	A [auth E], B [auth A]	149	Arabidopsis thaliana	Mutation(s): 1  Gene Names: NUDT1, NUDX1, At1g68760, F14K14.13 EC: 3.6.1.55 (PDB Primary Data), 3.6.1.67 (PDB Primary Data), 3.6.1.22 (PDB Primary Data)
UniProt
Find proteins for Q9CA40 (Arabidopsis thaliana) Explore Q9CA40  Go to UniProtKB:  Q9CA40

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth E], F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth E], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.213 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.658	α = 90
b = 117.306	β = 90
c = 68.937	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Liu, J., Guan, Z., Yan, L., Zou, T., Yin, P.

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description