Biological Assembly 1  

 3D View: Structure | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 55.31 kDa 
• Atom Count: 4215 
• Modelled Residue Count: 480 
• Deposited Residue Count: 480 
• Unique protein chains: 1

1UD2

Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38)

• DOI: 10.2210/pdb1UD2/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus sp. KSM-K38
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2003-04-28 Released: 2003-07-22 
• Deposition Author(s): Nonaka, T., Fujihashi, M., Kita, A., Hagihara, H., Ozaki, K., Ito, S., Miki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.229 
• R-Value Work: 0.196 

Literature

Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites

Nonaka, T., Fujihashi, M., Kita, A., Hagihara, H., Ozaki, K., Ito, S., Miki, K.

(2003) J Biol Chem 278: 24818-24824

• PubMed: 12719434 
• DOI: 10.1074/jbc.M212763200
• Primary Citation of Related Structures:  
  1UD2, 1UD3, 1UD4, 1UD5, 1UD6, 1UD8


• PubMed Abstract: 
  

The crystal structure of a calcium-free alpha-amylase (AmyK38) from Bacillus sp. strain KSM-K38, which resists chelating reagents and chemical oxidants, has been determined by the molecular replacement method and refined to a crystallographic R-factor of 19.9% (R-free of 23.2%) at 2.13-A resolution. The main chain folding of AmyK38 is almost homologous to that of Bacillus licheniformis alpha-amylase. However, neither a highly conserved calcium ion, which is located at the interface between domains A and B, nor any other calcium ions appear to exist in the AmyK38 molecule, although three sodium ions were found, one of which is located at the position corresponding to that of a highly conserved calcium ion of other alpha-amylases. The existence of these sodium ions was crystallographically confirmed by the structures of three metal-exchanged and mutated enzymes. This is the first case in which the structure of the calcium-free alpha-amylase has been determined by crystallography, and it was suggested that these sodium ions, instead of calcium ions, are used to retain the structure and function of AmyK38.

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Organizational Affiliation: 

Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
amylase	A	480	Bacillus sp. KSM-K38	Mutation(s): 0  Gene Names: amyK38 EC: 3.2.1.1
UniProt
Find proteins for Q93I48 (Bacillus sp. KSM-K38) Explore Q93I48  Go to UniProtKB:  Q93I48

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	B [auth A], C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.229 
• R-Value Work: 0.196 
• Space Group: P 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.143	α = 90
b = 132.143	β = 90
c = 132.143	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-28 
• Released Date: 2003-07-22 
Deposition Author(s): Nonaka, T., Fujihashi, M., Kita, A., Hagihara, H., Ozaki, K., Ito, S., Miki, K.

Revision History  

• Version 1.0: 2003-07-22
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance