5GP0 | pdb_00005gp0

Crystal structure of geraniol-NUDX1 complex

• PDB DOI: https://doi.org/10.2210/pdb5GP0/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-07-30 Released: 2017-10-04 
• Deposition Author(s): Liu, J., Guan, Z., Zou, T., Yin, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.210 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

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 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.
National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 67.77 kDa 
• Atom Count: 5,269 
• Modeled Residue Count: 552 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nudix hydrolase 1	A [auth E], B [auth F], C [auth I], D [auth A]	149	Arabidopsis thaliana	Mutation(s): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GPP	F [auth E], G [auth F], I, J [auth A]	GERANYL DIPHOSPHATE C10 H20 O7 P2 GVVPGTZRZFNKDS-JXMROGBWSA-N
GOL	E, H [auth I]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.210 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.761	α = 90
b = 83.582	β = 90
c = 116.36	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
XDS	data processing
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-04 
Deposition Author(s): Liu, J., Guan, Z., Zou, T., Yin, P.

Revision History  

• Version 1.0: 2017-10-04
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Database references
• Version 1.2: 2018-01-17
  Changes: Database references
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2023-11-08
  Changes: Data collection, Database references, Refinement description