3EDF

Structural base for cyclodextrin hydrolysis

• PDB DOI: https://doi.org/10.2210/pdb3EDF/pdb

• Classification: HYDROLASE
• Organism(s): Flavobacterium sp. 92
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-09-03 Released: 2009-03-03 
• Deposition Author(s): Buedenbender, S., Schulz, G.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.201 
• R-Value Work: 0.167 
• R-Value Observed: 0.167 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 140.54 kDa 
• Atom Count: 11,344 
• Modelled Residue Count: 1,194 
• Deposited Residue Count: 1,202 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclomaltodextrinase	A, B	601	Flavobacterium sp. 92	Mutation(s): 2  Gene Names: cdase EC: 3.2.1.54
UniProt
Find proteins for Q8KKG0 (Flavobacterium sp. 92) Explore Q8KKG0  Go to UniProtKB:  Q8KKG0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C, E	6		N/A
Glycosylation Resources
GlyTouCan:  G09454VW GlyCosmos:  G09454VW GlyGen:  G09454VW

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
Cyclohexakis-(1-4)-(alpha-D-glucopyranose)	D, F	6		N/A
Glycosylation Resources
GlyTouCan:  G22307HL GlyCosmos:  G22307HL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth A], J [auth A], M [auth B], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	G [auth A], H [auth A], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900020	C, E	beta-cellohexaose	Oligosaccharide / Metabolism

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900015	D, F	alpha-cyclodextrin	Oligosaccharide / Drug delivery

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.201 
• R-Value Work: 0.167 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.542	α = 90
b = 111.107	β = 90
c = 106.602	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-03 
Deposition Author(s): Buedenbender, S., Schulz, G.E.

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-11-10
  Changes: Database references, Structure summary