Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 60.79 kDa 
• Atom Count: 5098 
• Residue Count: 486 
• Unique protein chains: 1

2XFY

Crystal structure of Barley Beta-Amylase complexed with alpha- cyclodextrin

• DOI: 10.2210/pdb2XFY/pdb

• Classification: HYDROLASE
• Organism(s): Hordeum vulgare
• Mutation(s): No 


• Deposited: 2010-05-28 Released: 2010-12-01 
• Deposition Author(s): Rejzek, M., Stevenson, C.E.M., Southard, A.M., Stanley, D., Denyer, K., Smith, A.M., Naldrett, M.J., Lawson, D.M., Field, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.153 
• R-Value Work: 0.122 
• R-Value Observed: 0.124 

Literature

Chemical Genetics and Cereal Starch Metabolism: Structural Basis of the Non-Covalent and Covalent Inhibition of Barley Beta-Amylase.

Rejzek, M., Stevenson, C.E.M., Southard, A.M., Stanley, D., Denyer, K., Smith, A.M., Naldrett, M.J., Lawson, D.M., Field, R.A.

(2011) Mol Biosyst 7: 718

• PubMed: 21085740 
• DOI: 10.1039/c0mb00204f
• Structures With Same Primary Citation


• PubMed Abstract: 
  

There are major issues regarding the proposed pathway for starch degradation in germinating cereal grain. Given the commercial importance but genetic intractability of the problem, we have embarked on a program of chemical genetics studies to identify and dissect the pathway and regulation of starch degradation in germinating barley grains. As a precursor to in vivo studies, here we report systematic analysis of the reversible and irreversible inhibition of the major β-amylase of the grain endosperm (BMY1). The molecular basis of inhibitor action was defined through high resolution X-ray crystallography studies of unliganded barley β-amylase, as well as its complexes with glycone site binder disaccharide iminosugar G1M, irreversible inhibitors α-epoxypropyl and α-epoxybutyl glucosides, which target the enzyme's catalytic residues, and the aglycone site binders acarbose and α-cyclodextrin.

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Organizational Affiliation: 

Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
BETA-AMYLASE	A	535	Hordeum vulgare	Mutation(s): 0  Gene Names: BMY1, AMYB EC: 3.2.1.2
Find proteins for P16098 (Hordeum vulgare) Explore P16098  Go to UniProtKB:  P16098

Oligosaccharides

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram
Cyclohexakis-(1-4)-(alpha-D-glucopyranose)	A	6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.153 
• R-Value Work: 0.122 
• R-Value Observed: 0.124 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.846	α = 90
b = 71.466	β = 90
c = 92.472	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-05-28 
• Released Date: 2010-12-01 
Deposition Author(s): Rejzek, M., Stevenson, C.E.M., Southard, A.M., Stanley, D., Denyer, K., Smith, A.M., Naldrett, M.J., Lawson, D.M., Field, R.A.

Revision History 

• Version 1.0: 2010-12-01
  Type: Initial release
  
• Version 1.1: 2012-01-11
  Changes: Database references, Refinement description, Version format compliance
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2019-05-22
  Changes: Data collection, Experimental preparation
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary