7WWC | pdb_00007wwc

Crystal structure of beta-1,3(4)-glucanase with Laminaritriose

PDB DOI: https://doi.org/10.2210/pdb7WWC/pdb

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

Deposited: 2022-02-12 Released: 2023-02-15
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: 2.20 Å
R-Value Free:
0.242 (Depositor), 0.240 (DCC)
R-Value Work:
0.191 (Depositor), 0.180 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of beta-1,3(4)-glucanase with Laminaritriose

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

To be published.

Macromolecule Content

Total Structure Weight: 55.71 kDa
Atom Count: 4,101
Modeled Residue Count: 479
Deposited Residue Count: 479
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(4)-glucanase	A	479	Pedobacter sp.	Mutation(s): 0
UniProt
Find proteins for A0A1G7XNR7 (Pedobacter terrae) Explore A0A1G7XNR7 Go to UniProtKB: A0A1G7XNR7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1G7XNR7
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	B [auth D]	2		N/A	Interactions Focus chain B [auth D] Interactions & Density Focus chain B [auth D]
Glycosylation Resources
GlyTouCan: G36535HU GlyCosmos: G36535HU

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	C [auth B]	3		N/A	Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
Glycosylation Resources
GlyTouCan: G00024MO GlyCosmos: G00024MO GlyGen: G00024MO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.242 (Depositor), 0.240 (DCC)
R-Value Work: 0.191 (Depositor), 0.180 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.648	α = 90
b = 120.648	β = 90
c = 69.966	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-02-15

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: 2023-02-15
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.