3BMW

Cyclodextrin glycosyl transferase from Thermoanerobacterium thermosulfurigenes EM1 mutant S77P complexed with a maltoheptaose inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3BMW/pdb

• Classification: TRANSFERASE
• Organism(s): Thermoanaerobacterium thermosulfurigenes
• Expression System: Bacillus subtilis
• Mutation(s): Yes 


• Deposited: 2007-12-13 Released: 2008-05-27 
• Deposition Author(s): Rozeboom, H.J., van Oosterwijk, N., Dijkstra, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.165 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 77.97 kDa 
• Atom Count: 6,689 
• Modelled Residue Count: 683 
• Deposited Residue Count: 683 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclomaltodextrin glucanotransferase	A	683	Thermoanaerobacterium thermosulfurigenes	Mutation(s): 1  Gene Names: amyA EC: 2.4.1.19
UniProt
Find proteins for P26827 (Thermoanaerobacterium thermosulfurigenes) Explore P26827  Go to UniProtKB:  P26827

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan:  G31885RT GlyCosmos:  G31885RT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	D	3		N/A
Glycosylation Resources
GlyTouCan:  G96370VA GlyCosmos:  G96370VA GlyGen:  G96370VA

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACI	E [auth A]	6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL C7 H13 N O4 XPHOBMULWMGEBA-VZFHVOOUSA-N
SO4	I [auth A], J [auth A], K [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900009	D	alpha-maltotriose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.165 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.791	α = 90
b = 96.582	β = 90
c = 115.241	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Rozeboom, H.J., van Oosterwijk, N., Dijkstra, B.W.

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2017-10-25
  Changes: Advisory, Atomic model, Derived calculations, Structure summary
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2021-11-10
  Changes: Database references, Structure summary
• Version 3.2: 2023-11-01
  Changes: Data collection, Refinement description
• Version 3.3: 2023-11-29
  Changes: Database references