6TVK | pdb_00006tvk

Alpha-L-fucosidase isoenzyme 2 from Paenibacillus thiaminolyticus

PDB DOI: https://doi.org/10.2210/pdb6TVK/pdb

Classification: HYDROLASE
Organism(s): Paenibacillus thiaminolyticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-01-09 Released: 2021-07-21
Deposition Author(s): Kovalova, T., Koval, T., Lipovova, P., Dohnalek, J.
Funding Organization(s): Czech Academy of Sciences, European Regional Development Fund, Ministry of Education, Youth and Sports of the Czech Republic

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.225 (Depositor), 0.205 (DCC)
R-Value Work:
0.189 (Depositor), 0.196 (DCC)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The first structure-function study of GH151 alpha-l-fucosidase uncovers new oligomerization pattern, active site complementation, and selective substrate specificity

Koval'ova, T., Koval, T., Stransky, J., Kolenko, P., Duskova, J., Svecova, L., Vodickova, P., Spiwok, V., Benesova, E., Lipovova, P., Dohnalek, J.

(2022) FEBS J

DOI: https://doi.org/10.1111/febs.16387

Macromolecule Content

Total Structure Weight: 80.33 kDa
Atom Count: 5,648
Modeled Residue Count: 660
Deposited Residue Count: 689
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-L-fucosidase	A [auth AAA]	689	Paenibacillus thiaminolyticus	Mutation(s): 0 Gene Names: aLfuk2, NCTC11027_00201
UniProt
Find proteins for K0JCW6 (Paenibacillus thiaminolyticus) Explore K0JCW6 Go to UniProtKB: K0JCW6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K0JCW6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TBR Query on TBR Download:Ideal Coordinates CCD File SDF format, chain B [auth AAA] MOL2 format, chain B [auth AAA] mmCIF format, chain B [auth AAA]	B [auth AAA]	HEXATANTALUM DODECABROMIDE Br₁₂ Ta₆ YWYIQTPPCOBSGN-UHFFFAOYSA-M		Interactions Focus chain B [auth AAA] Interactions & Density Focus chain B [auth AAA]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth AAA] MOL2 format, chain G [auth AAA] mmCIF format, chain G [auth AAA]	G [auth AAA]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth AAA] Interactions & Density Focus chain G [auth AAA]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain E [auth AAA] SDF format, chain D [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain D [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain D [auth AAA]	D [auth AAA], E [auth AAA], F [auth AAA]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A [auth AAA]	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.225 (Depositor), 0.205 (DCC)
R-Value Work: 0.189 (Depositor), 0.196 (DCC)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.118	α = 90
b = 125.118	β = 90
c = 231.905	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
AutoSol	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-07-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Czech Academy of Sciences	Czech Republic	86652036
European Regional Development Fund	Czech Republic	CZ.02.1.01/0.0/0.0/15_003/0000447
European Regional Development Fund	Czech Republic	CZ.02.1.01/0.0/0.0/16_013/0001776
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LM2015043
European Regional Development Fund	Czech Republic	CZ.1.05/1.1.00/02.0109

Revision History (Full details and data files)

Version 1.0: 2021-07-21
Type: Initial release
Version 1.1: 2022-05-18
Changes: Database references
Version 1.2: 2024-10-23
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2026-09-02
Type: Remediation
Reason: Metalloprotein remediation
Changes: Derived calculations