5Z0T

Thermoactinomyces vulgaris R-47 alpha-amylase I (TVA I) mutant A357V/Q359N/Y360E (AQY/VNE)

• PDB DOI: https://doi.org/10.2210/pdb5Z0T/pdb

• Classification: HYDROLASE
• Organism(s): Thermoactinomyces vulgaris
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-12-21 Released: 2018-02-21 
• Deposition Author(s): Tonozuka, T.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.184 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Literature

Mutagenesis-induced conformational change in domain B of a pullulan-hydrolyzing alpha-amylase TVA I

Tonozuka, T., Nihira, T., Mizuno, M., Nishikawa, A., Kamitori, S.

(2018) Amylase 2: 1-10

• DOI: https://doi.org/10.1515/amylase-2018-0001

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 142.66 kDa 
• Atom Count: 12,061 
• Modelled Residue Count: 1,274 
• Deposited Residue Count: 1,274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neopullulanase 1	A, B	637	Thermoactinomyces vulgaris	Mutation(s): 3  Gene Names: tvaI EC: 3.2.1.135
UniProt
Find proteins for Q60053 (Thermoactinomyces vulgaris) Explore Q60053  Go to UniProtKB:  Q60053

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	F [auth A], J [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.184 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.886	α = 90
b = 50.749	β = 103.91
c = 121.897	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-02-21 
Deposition Author(s): Tonozuka, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	16K07687

Revision History  

• Version 1.0: 2018-02-21
  Type: Initial release
  
• Version 1.1: 2018-03-28
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description