2D0H

Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N/E396Q complexed with P2, a pullulan model oligosaccharide

• PDB DOI: https://doi.org/10.2210/pdb2D0H/pdb

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


• Deposited: 2005-08-02 Released: 2006-07-11 
• Deposition Author(s): Abe, A., Yoshida, H., Tonozuka, T., Sakano, Y., Kamitori, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.200 
• R-Value Work: 0.156 
• R-Value Observed: 0.161 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 72.34 kDa 
• Atom Count: 5,499 
• Modelled Residue Count: 637 
• Deposited Residue Count: 637 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-amylase I	A	637	Thermoactinomyces vulgaris	Mutation(s): 2  EC: 3.2.1.1
UniProt
Find proteins for Q60053 (Thermoactinomyces vulgaris) Explore Q60053  Go to UniProtKB:  Q60053

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	6		N/A
Glycosylation Resources
GlyTouCan:  G84547LV GlyCosmos:  G84547LV GlyGen:  G84547LV

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.200 
• R-Value Work: 0.156 
• R-Value Observed: 0.161 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.45	α = 90
b = 92.29	β = 91.35
c = 55.89	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-11 
Deposition Author(s): Abe, A., Yoshida, H., Tonozuka, T., Sakano, Y., Kamitori, S.

Revision History  

• Version 1.0: 2006-07-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-11-10
  Changes: Database references, Structure summary