9HE8 | pdb_00009he8

The molecular structure of a beta-1,4-D-xylosidase from the probiotic bacterium Levilactobacillus brevis

• PDB DOI: https://doi.org/10.2210/pdb9HE8/pdb

• Classification: CARBOHYDRATE
• Organism(s): Levilactobacillus brevis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-13 Released: 2025-01-15 
• Deposition Author(s): Linares-Pasten, J., Logan, D.T., Nordberg Karlsson, E.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.241 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.218 (DCC) 

Starting Model: experimental

Literature

The molecular strcuture of a beta-1,4-D-xylosidase from the probiotic bacterium Levilactobacillus brevis

Linares-Pasten, J., Logan, D.T., Nordberg Karlsson, E.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 254.58 kDa 
• Atom Count: 18,316 
• Modeled Residue Count: 2,168 
• Deposited Residue Count: 2,240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylosidase	A, B, C, D	560	Levilactobacillus brevis	Mutation(s): 0  Gene Names: xynB46, UCCLBBS449_2475 EC: 3.2.1.37
UniProt
Find proteins for A0A1L7HA01 (Levilactobacillus brevis) Explore A0A1L7HA01  Go to UniProtKB:  A0A1L7HA01

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.241 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.218 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.429	α = 90
b = 177.18	β = 98.844
c = 78.753	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Linares-Pasten, J., Logan, D.T., Nordberg Karlsson, E.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2014-05038

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release