1DED

CRYSTAL STRUCTURE OF ALKALOPHILIC ASPARAGINE 233-REPLACED CYCLODEXTRIN GLUCANOTRANSFERASE COMPLEXED WITH AN INHIBITOR, ACARBOSE, AT 2.0 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1DED/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus sp. 1011
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-11-14 Released: 2000-04-07 
• Deposition Author(s): Ishii, N., Haga, K., Yamane, K., Harata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.222 
• R-Value Work: 0.163 
• R-Value Observed: 0.163 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 152.51 kDa 
• Atom Count: 11,515 
• Modelled Residue Count: 1,372 
• Deposited Residue Count: 1,372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLODEXTRIN GLUCANOTRANSFERASE	A, B	686	Bacillus sp. 1011	Mutation(s): 1  EC: 2.4.1.19
UniProt
Find proteins for P05618 (Bacillus sp. (strain 1011)) Explore P05618  Go to UniProtKB:  P05618

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)-beta-D-glucopyranose	C, D, E	3	N/A	N/A
Glycosylation Resources
GlyTouCan:  G08743RW GlyCosmos:  G08743RW

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	F [auth A], G [auth A], H [auth B], I [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_900022	C, D, E	beta-acarbose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.222 
• R-Value Work: 0.163 
• R-Value Observed: 0.163 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.93	α = 85.1
b = 73.83	β = 105.4
c = 79.05	γ = 100.5

Software Package:

Software Name	Purpose
MADNESS	data collection
X-PLOR	model building
X-PLOR	refinement
MADNESS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-04-07 
Deposition Author(s): Ishii, N., Haga, K., Yamane, K., Harata, K.

Revision History  

• Version 1.0: 2000-04-07
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2018-04-18
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-11-03
  Changes: Database references, Structure summary