7E9X | pdb_00007e9x

Trehalase of Arabidopsis thaliana acid mutant -D380A

• PDB DOI: https://doi.org/10.2210/pdb7E9X/pdb

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


• Deposited: 2021-03-05 Released: 2022-03-09 
• Deposition Author(s): Taguchi, Y., Saburi, W., Yu, J., Imai, R., Yao, M., Mori, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.245 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

pH-dependent alteration of substrate specificity of plant trehalase and its molecular mechanism

Taguchi, Y., Saburi, W., Yu, J., Imai, R., Yao, M., Mori, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 260.83 kDa 
• Atom Count: 18,502 
• Modeled Residue Count: 2,187 
• Deposited Residue Count: 2,288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trehalase	A, B, C, D	572	Arabidopsis thaliana	Mutation(s): 1  Gene Names: TRE1, At4g24040, T19F6.15, T19F6.30 EC: 3.2.1.28
UniProt
Find proteins for Q9SU50 (Arabidopsis thaliana) Explore Q9SU50  Go to UniProtKB:  Q9SU50

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.245 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.657	α = 90
b = 129.647	β = 91.027
c = 151.141	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-09 
Deposition Author(s): Taguchi, Y., Saburi, W., Yu, J., Imai, R., Yao, M., Mori, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18J20503

Revision History  

• Version 1.0: 2022-03-09
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description