7VTL | pdb_00007vtl

Crystal structure of GH family 64 beta-1,3-glucanase complexed with Laminaritriose

PDB DOI: https://doi.org/10.2210/pdb7VTL/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: 2.07 Å
R-Value Free:
0.229 (Depositor), 0.230 (DCC)
R-Value Work:
0.208 (Depositor), 0.210 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of GH family 64 beta-1,3-glucanase complexed with Laminaritriose

Jiang, Z.Q., Ma, J.W.

To be published.

Macromolecule Content

Total Structure Weight: 41.25 kDa
Atom Count: 3,052
Modeled Residue Count: 373
Deposited Residue Count: 373
Unique protein chains: 1

Macromolecules

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(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	B, C	2		N/A	Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900115 Query on PRD_900115	B, C	4beta-beta-mannobiose	Oligosaccharide / Metabolism		Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.229 (Depositor), 0.230 (DCC)
R-Value Work: 0.208 (Depositor), 0.210 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.68	α = 90
b = 81.68	β = 90
c = 161.24	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.