8HVB

Crystal structure of lacto-N-biosidase StrLNBase from Streptomyces sp. strain 142, lacto-N-biose complex

• PDB DOI: https://doi.org/10.2210/pdb8HVB/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces sp.
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-12-26 Released: 2023-12-27 
• Deposition Author(s): Fushinobu, S., Yamada, C., Fujio, N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.184 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 

Starting Model: experimental

Literature

Crystal structure of glycoside hydrolase family 20 lacto-N-biosidase from soil bacterium Streptomyces sp. strain 142

Fujio, N., Yamada, C., Fushinobu, S.

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

Macromolecule Content

• Total Structure Weight: 66.64 kDa 
• Atom Count: 5,042 
• Modelled Residue Count: 601 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lacto-N-biosidase	A	614	Streptomyces sp.	Mutation(s): 0
UniProt
Find proteins for Q9Z4I7 (Streptomyces sp) Explore Q9Z4I7  Go to UniProtKB:  Q9Z4I7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDG	C [auth A]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
GAL	B [auth A]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.184 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.925	α = 90
b = 51.344	β = 98.03
c = 86.507	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Fushinobu, S., Yamada, C., Fujio, N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release