1W9X

Bacillus halmapalus alpha amylase

• PDB DOI: https://doi.org/10.2210/pdb1W9X/pdb

• Classification: HYDROLASE
• Organism(s): Sutcliffiella halmapala
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2004-10-20 Released: 2005-02-09 
• Deposition Author(s): Davies, G.J., Brzozowski, A.M., Dauter, Z., Rasmussen, M.D., Borchert, T.V., Wilson, K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.198 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 

Literature

Structure of a Bacillus Halmapalus Family 13 Alpha-Amylase, Bha, in Complex with an Acarbose-Derived Nonasaccharide at 2.1 A Resolution

Davies, G.J., Brzozowski, A.M., Dauter, Z., Rasmussen, M.D., Borchert, T.V., Wilson, K.S.

(2005) Acta Crystallogr D Biol Crystallogr 61: 190

• PubMed: 15681870 
• DOI: https://doi.org/10.1107/S0907444904027118
• Primary Citation of Related Structures:  
  1W9X


• PubMed Abstract: 
  

  The enzymatic digestion of starch by alpha-amylases is one of the key biotechnological reactions of recent times. In the search for industrial biocatalysts, the family GH13 alpha-amylase BHA from Bacillus halmapalus has been cloned and expressed. The three-dimensional structure at 2.1 A resolution has been determined in complex with the (pseudo)tetrasaccharide inhibitor acarbose. Acarbose is found bound as a nonasaccharide transglycosylation product spanning the -6 to +3 subsites. Careful inspection of electron density suggests that the bound ligand could not have been formed through successive transglycosylations of acarbose and must also have featured maltose or maltooligosaccharides as an acceptor.

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Organizational Affiliation: 

Department of Chemistry, University of York, England. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 56.86 kDa 
• Atom Count: 4,300 
• Modelled Residue Count: 481 
• Deposited Residue Count: 481 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA AMYLASE	A	481	Sutcliffiella halmapala	Mutation(s): 0  EC: 3.2.1.1
UniProt
Find proteins for O82839 (Bacillus sp) Explore O82839  Go to UniProtKB:  O82839

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	7	N/A	N/A
Glycosylation Resources
GlyTouCan:  G14192NX GlyCosmos:  G14192NX

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.198 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.18	α = 90
b = 75.847	β = 90
c = 155.23	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-09 
Deposition Author(s): Davies, G.J., Brzozowski, A.M., Dauter, Z., Rasmussen, M.D., Borchert, T.V., Wilson, K.S.

Revision History  

• Version 1.0: 2005-02-09
  Type: Initial release
  
• Version 1.1: 2011-05-08
  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, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary