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

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Z4I7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDG Query on NDG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	2-acetamido-2-deoxy-alpha-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-PVFLNQBWSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GAL Query on GAL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.