9JOF | pdb_00009jof

COMPLEX STRUCTURE OF ENDO-1,3-FUCANASE (FUN168D) FROM GH168 FAMILY WITH FUCOTRIOSE

PDB DOI: https://doi.org/10.2210/pdb9JOF/pdb

Classification: HYDROLASE
Organism(s): Wenyingzhuangia fucanilytica
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-24 Released: 2024-11-27
Deposition Author(s): Chen, G.N., Chang, Y.G.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.169 (Depositor), 0.167 (DCC)
R-Value Work:
0.141 (Depositor), 0.141 (DCC)
R-Value Observed:
0.141 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Complex structure of endo-1.3-fucanase (Fun168D) from GH168 family with fucotriose at 1.50 Angstroms resulution.

Chen, G.N., Chang, Y.G.

To be published.

Macromolecule Content

Total Structure Weight: 97.4 kDa
Atom Count: 7,354
Modeled Residue Count: 736
Deposited Residue Count: 846
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
endo-1.3-fucanase	A, B	423	Wenyingzhuangia fucanilytica	Mutation(s): 0 Gene Names: AXE80_08865
UniProt
Find proteins for A0A1B1Y6G8 (Wenyingzhuangia fucanilytica) Explore A0A1B1Y6G8 Go to UniProtKB: A0A1B1Y6G8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1B1Y6G8
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-2,4-di-O-sulfo-alpha-L-fucopyranose-(1-3)-2-O-sulfo-alpha-L-fucopyranose	C, D	3		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.169 (Depositor), 0.167 (DCC)
R-Value Work: 0.141 (Depositor), 0.141 (DCC)
R-Value Observed: 0.141 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.819	α = 90
b = 138.329	β = 113.79
c = 63.062	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	U22A20542

Revision History (Full details and data files)

Version 1.0: 2024-11-27
Type: Initial release

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.