9UL7 | pdb_00009ul7

Improved thermostability of a GH3 glycosidase based on its X-ray crystal structure

• PDB DOI: https://doi.org/10.2210/pdb9UL7/pdb

• Classification: HYDROLASE
• Organism(s): Clavibacter michiganensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-04-19 Released: 2025-06-11 
• Deposition Author(s): Dong, P.P., Dong, P.P.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.236 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: in silico

Literature

Improved thermostability of a GH3 glycosidase based on its X-ray crystal structure

Dong, P.P., Dong, P.P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 67.84 kDa 
• Atom Count: 4,877 
• Modeled Residue Count: 601 
• Deposited Residue Count: 620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-glucosidase	A	620	Clavibacter michiganensis	Mutation(s): 0  Gene Names: bglX_1, BFL34_01020 EC: 3.2.1.21
UniProt
Find proteins for A5CPI7 (Clavibacter michiganensis subsp. michiganensis (strain NCPPB 382)) Explore A5CPI7  Go to UniProtKB:  A5CPI7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.236 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.866	α = 90
b = 104.617	β = 91.91
c = 69.156	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Dong, P.P., Dong, P.P.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release