9JOO | pdb_00009joo

COMPLEX STRUCTURE OF ENDO-1,3-FUCANASE (FUN168E) WITH FUCOTETRAOSES

PDB DOI: https://doi.org/10.2210/pdb9JOO/pdb

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

Deposited: 2024-09-25 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: 1.97 Å
R-Value Free:
0.221 (Depositor), 0.205 (DCC)
R-Value Work:
0.182 (Depositor)
R-Value Observed:
0.184 (Depositor)

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

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

Literature

Complex structure of endo-1.3-fucanase (Fun168E) with fucotetraoses at 1.97 Angstroms resulution.

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

To be published.

Macromolecule Content

Total Structure Weight: 47.42 kDa
Atom Count: 3,389
Modeled Residue Count: 357
Deposited Residue Count: 394
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein	A	394	Wenyingzhuangia fucanilytica	Mutation(s): 0 Gene Names: AXE80_08855
UniProt
Find proteins for A0A1B1Y6K9 (Wenyingzhuangia fucanilytica) Explore A0A1B1Y6K9 Go to UniProtKB: A0A1B1Y6K9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1B1Y6K9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.221 (Depositor), 0.205 (DCC)
R-Value Work: 0.182 (Depositor)
R-Value Observed: 0.184 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.45	α = 90
b = 79.56	β = 90
c = 81.83	γ = 90

Software Package:

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

Structure Validation

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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

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