3WA7 | pdb_00003wa7

Crystal structure of selenomethionine-labeled tannase from Lactobacillus plantarum in the orthorhombic crystal

• PDB DOI: https://doi.org/10.2210/pdb3WA7/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.193 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

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 
• DOI: https://doi.org/10.1002/prot.24355
• Primary Citation 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.6 kDa 
• Atom Count: 3,975 
• Modeled Residue Count: 467 
• Deposited Residue Count: 477 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.193 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.73	α = 90
b = 77.82	β = 90
c = 199.05	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Matoba, Y., Tanaka, N., Sugiyama, M.

Revision History  

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