1WZA

Crystal structure of alpha-amylase from H.orenii

• PDB DOI: https://doi.org/10.2210/pdb1WZA/pdb

• Classification: HYDROLASE
• Organism(s): Halothermothrix orenii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-03-03 Released: 2006-04-11 
• Deposition Author(s): Sivakumar, N., Swaminathan, K., Li, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of AmyA lacks acidic surface and provide insights into protein stability at poly-extreme condition.

Sivakumar, N., Li, N., Tang, J.W., Patel, B.K., Swaminathan, K.

(2006) FEBS Lett 580: 2646-2652

• PubMed: 16647060 
• DOI: https://doi.org/10.1016/j.febslet.2006.04.017
• Primary Citation of Related Structures:  
  1WZA


• PubMed Abstract: 
  

  Here we report the first crystal structure of a protein, AmyA, a secretory alpha-amylase isolated from Halothermothrix orenii, which is both halophilic and thermophilic. The crystal structure was determined at 1.6 A resolution. AmyA lacks the conserved acidic surface, which is considered essential for protein stability at high salinity. Sedimentation velocity and CD experiments on AmyA reveal the formation of unique reversible poly-dispersed oligomers that show unusually high thermal stability. These studies provide valuable insight into the structural elements that contribute to the stability of AmyA at both physical and chemical extremes and their functional implications.

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Organizational Affiliation: 

Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 56.83 kDa 
• Atom Count: 4,578 
• Modelled Residue Count: 488 
• Deposited Residue Count: 488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-amylase A	A	488	Halothermothrix orenii	Mutation(s): 0  Gene Names: AMYA EC: 3.2.1.1
UniProt
Find proteins for Q8GPL8 (Halothermothrix orenii) Explore Q8GPL8  Go to UniProtKB:  Q8GPL8

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.126	α = 90
b = 61.658	β = 90
c = 147.625	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-11 
Deposition Author(s): Sivakumar, N., Swaminathan, K., Li, N.

Revision History  

• Version 1.0: 2006-04-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description