7VTM

Crystal structure of Glucoside hydrolase family 64 beta-1,3-glucanase complexed with Laminaritetraose

PDB DOI: https://doi.org/10.2210/pdb7VTM/pdb

Classification: HYDROLASE
Organism(s): Streptomyces pratensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-10-29 Released: 2022-11-02
Deposition Author(s): Jiang, Z.Q., Ma, J.W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.228
R-Value Work: 0.211
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 41.57 kDa
Atom Count: 3,228
Modelled Residue Count: 373
Deposited Residue Count: 373
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-1,3-Glucanase	A	373	Streptomyces pratensis	Mutation(s): 0
UniProt
Find proteins for A0A8D3WIQ3 (Streptomyces pratensis (strain ATCC 33331 / IAF-45CD)) Explore A0A8D3WIQ3 Go to UniProtKB: A0A8D3WIQ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8D3WIQ3
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose	B, C	3		N/A	Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C
Glycosylation Resources
GlyTouCan: G03096YC GlyCosmos: G03096YC

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.228
R-Value Work: 0.211
R-Value Observed: 0.212
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.486	α = 90
b = 79.486	β = 90
c = 156.662	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	model building
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2022-11-02
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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.