3WA6

Crystal structure of tannase from Lactobacillus plantarum in the orthorhombic crystal

PDB DOI: https://doi.org/10.2210/pdb3WA6/pdb

Classification: HYDROLASE
Organism(s): Lactiplantibacillus plantarum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-04-27 Released: 2013-07-24
Deposition Author(s): Matoba, Y., Tanaka, N., Sugiyama, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.207
R-Value Work: 0.178
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystallographic and mutational analyses of tannase from Lactobacillus plantarum

Matoba, Y., Tanaka, N., Noda, M., Higashikawa, F., Kumagai, T., Sugiyama, M.

(2013) Proteins 81: 2052-2058

PubMed: 23836494 Search on PubMed
DOI: https://doi.org/10.1002/prot.24355
Primary Citation of Related Structures:
3WA6, 3WA7

PubMed Abstract:
Tannin acylhydrolase (EC 3.1.1.20) referred commonly as tannase catalyzes the hydrolysis of the galloyl ester bond of tannins to release gallic acid. Although the enzyme is useful for various industries, the tertiary structure is not yet determined. In this study, we determined the crystal structure of tannase produced by Lactobacillus plantarum. The tannase structure belongs to a member of α/β-hydrolase superfamily with an additional "lid" domain. A glycerol molecule derived from cryoprotectant solution was accommodated into the tannase active site. The binding manner of glycerol to tannase seems to be similar to that of the galloyl moiety in the substrate.

Organizational Affiliation

Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551, Japan.

Macromolecule Content

Total Structure Weight: 52.03 kDa
Atom Count: 3,912
Modelled Residue Count: 466
Deposited Residue Count: 477
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tannase	A	477	Lactiplantibacillus plantarum	Mutation(s): 0 EC: 3.1.1.20
UniProt
Find proteins for B3Y018 (Lactiplantibacillus plantarum) Explore B3Y018 Go to UniProtKB: B3Y018
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B3Y018
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.207
R-Value Work: 0.178
R-Value Observed: 0.178
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.87	α = 90
b = 78.24	β = 90
c = 200.01	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHARP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-07-24

Deposition Author(s):

Matoba, Y.

Tanaka, N.

Sugiyama, M.

Revision History (Full details and data files)

Version 1.0: 2013-07-24
Type: Initial release
Version 1.1: 2013-11-06
Changes: Database references
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations