5AXH

Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus, D312G mutant in complex with isomaltohexaose

• PDB DOI: https://doi.org/10.2210/pdb5AXH/pdb

• Classification: HYDROLASE
• Organism(s): Thermoanaerobacter pseudethanolicus ATCC 33223
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-07-29 Released: 2015-11-11 
• Deposition Author(s): Suzuki, N., Kishine, N., Fujimoto, Z., Sakurai, M., Momma, M., Ko, J.A., Nam, S.H., Kimura, A., Kim, Y.M.
• Funding Organization(s): Ministry of Agriculture, Forestry and Fisheries, National Research Foundation of Korea

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.205 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

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: 144.88 kDa 
• Atom Count: 10,326 
• Modelled Residue Count: 1,173 
• Deposited Residue Count: 1,236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dextranase	A, B	618	Thermoanaerobacter pseudethanolicus ATCC 33223	Mutation(s): 1  Gene Names: Teth39_0264 EC: 3.2.1.11
UniProt
Find proteins for B0KBZ7 (Thermoanaerobacter pseudethanolicus (strain ATCC 33223 / 39E)) Explore B0KBZ7  Go to UniProtKB:  B0KBZ7

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose	C	4		N/A
Glycosylation Resources
GlyTouCan:  G80662SX GlyCosmos:  G80662SX GlyGen:  G80662SX

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose	D	6		N/A
Glycosylation Resources
GlyTouCan:  G26640RK GlyCosmos:  G26640RK GlyGen:  G26640RK

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth A], I [auth B], J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.205 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.334	α = 90
b = 99.179	β = 90
c = 169.254	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-11-11 
Deposition Author(s): Suzuki, N., Kishine, N., Fujimoto, Z., Sakurai, M., Momma, M., Ko, J.A., Nam, S.H., Kimura, A., Kim, Y.M.

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Funding Organization	Location	Grant Number
Ministry of Agriculture, Forestry and Fisheries	Japan	25001A
National Research Foundation of Korea	Korea, Republic Of	2010-0020141

Revision History  

• Version 1.0: 2015-11-11
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Database references
• Version 1.2: 2020-02-26
  Changes: Data collection, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary