8HVD

Crystal structure of lacto-N-biosidase StrLNBase from Streptomyces sp. strain 142, galacto-N-biose complex 2

• PDB DOI: https://doi.org/10.2210/pdb8HVD/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: 1.41 Å
• R-Value Free: 0.193 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

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: 66.62 kDa 
• Atom Count: 5,378 
• Modelled Residue Count: 602 
• 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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G00031MO GlyCosmos:  G00031MO GlyGen:  G00031MO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.193 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.779	α = 90
b = 60.825	β = 98.19
c = 88.232	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