8I0X | pdb_00008i0x

Beta-Xylosidase JB13GH39P28 showing salt/ethanol/trypsin tolerance, low-pH/low-Temperature activity, and transformation of notoginsenosides

• PDB DOI: https://doi.org/10.2210/pdb8I0X/pdb

• Classification: HYDROLASE
• Organism(s): Sphingomonas sp.
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2023-01-11 Released: 2024-04-24 
• Deposition Author(s): Zhou, J.P., Cao, L.J., Lin, M.Y., Zhang, R., Huang, Z.X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

beta-Xylosidase JB13GH39P28(D41G)showing salt/ethanol/trypsin tolerance and transformation of notoginsenosides

Cao, L.J., Lin, M.Y., Zhang, R., Huang, Z.X., Zhou, J.P.

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.

Macromolecule Content 

• Total Structure Weight: 116.66 kDa 
• Atom Count: 8,814 
• Modeled Residue Count: 990 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 39 beta-xylosidase	A [auth B], B [auth A]	520	Sphingomonas sp.	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.403	α = 90
b = 62.627	β = 91.419
c = 140.117	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Zhou, J.P., Cao, L.J., Lin, M.Y., Zhang, R., Huang, Z.X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release