6IFE | pdb_00006ife

A Glycoside Hydrolase Family 43 beta-Xylosidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.199 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Biochemical and structural properties of a low-temperature-active glycoside hydrolase family 43 beta-xylosidase: Activity and instability at high neutral salt concentrations.

Zhang, R.Li, N.Liu, Y.Han, X.Tu, T.Shen, J.Xu, S.Wu, Q.Zhou, J.Huang, Z.

(2019) Food Chem 301: 125266-125266

  • DOI: https://doi.org/10.1016/j.foodchem.2019.125266
  • Primary Citation Related Structures: 
    6IFE

  • PubMed Abstract: 

    β-Xylosidase, of the glycoside hydrolase family 43 from Bacillus sp. HJ14, was expressed in Escherichia coli. Recombinant β-xylosidase (rHJ14GH43) exhibited maximum activity at 25 °C, approximately 15, 45, and 88% of maximum activity at 0, 10, and 20 °C, respectively, and poor stability at temperatures over 20 °C. rHJ14GH43 showed moderate or high activity, but poor stability, in NaCl, KCl, NaNO 3 , KNO 3 , Na 2 SO 4 , and (NH 4 ) 2 SO 4 at concentrations from 3.0 to 30.0% (w/v). The crystal structure of rHJ14GH43 was resolved and showed higher structural flexibility due to fewer salt bridges and hydrogen bonds compared to mesophilic and thermophilic β-xylosidases. High structural flexibility is presumed to be a key factor for catalytic adaptations to low temperatures and high salt concentrations. Approximately one-third of the surface of rHJ14GH43 is positively charged, which may be the primary factor responsible for poor stability in high neutral salt environments.


  • Organizational Affiliation
    • Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, PR China; College of Life Sciences, Yunnan Normal University, Kunming 650500, PR China; Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan, Kunming 650500, PR China.

Macromolecule Content 

  • Total Structure Weight: 127.67 kDa 
  • Atom Count: 9,111 
  • Modeled Residue Count: 1,069 
  • Deposited Residue Count: 1,106 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-xylosidase
A, B
553Bacillus pumilusMutation(s): 0 
Gene Names: B4107_1875
EC: 3.2.1.37
UniProt
Find proteins for A0A4V8GZZ0 (Bacillus pumilus)
Explore A0A4V8GZZ0 
Go to UniProtKB:  A0A4V8GZZ0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4V8GZZ0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.199 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.637α = 90
b = 106.135β = 122.51
c = 105.884γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31660445

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-02
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description