1VFM

Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/alpha-cyclodextrin complex

• PDB DOI: https://doi.org/10.2210/pdb1VFM/pdb

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


• Deposited: 2004-04-16 Released: 2005-02-08 
• Deposition Author(s): Ohtaki, A., Mizuno, M., Tonozuka, T., Sakano, Y., Kamitori, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.248 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 137.17 kDa 
• Atom Count: 9,924 
• Modelled Residue Count: 1,170 
• Deposited Residue Count: 1,170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neopullulanase 2	A, B	585	Thermoactinomyces vulgaris	Mutation(s): 2  EC: 3.2.1.135
UniProt
Find proteins for Q08751 (Thermoactinomyces vulgaris) Explore Q08751  Go to UniProtKB:  Q08751

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
Cyclohexakis-(1-4)-(alpha-D-glucopyranose)	C	6		N/A
Glycosylation Resources
GlyTouCan:  G22307HL GlyCosmos:  G22307HL

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
Cyclic beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	D	6		N/A
Glycosylation Resources
GlyTouCan:  G22307HL GlyCosmos:  G22307HL

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900015	C	alpha-cyclodextrin	Oligosaccharide / Drug delivery

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.248 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.395	α = 90
b = 118.428	β = 90
c = 113.69	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-08 
Deposition Author(s): Ohtaki, A., Mizuno, M., Tonozuka, T., Sakano, Y., Kamitori, S.

Revision History  

• Version 1.0: 2005-02-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  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
• Version 2.2: 2023-12-27
  Changes: Data collection