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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 37.41 kDa 
• Atom Count: 2847 
• Modelled Residue Count: 315 
• Deposited Residue Count: 321 
• Unique protein chains: 1

6A8H

Crystal structure of endo-arabinanase ABN-TS D27A mutant in complex with arabinotriose

• DOI: 10.2210/pdb6A8H/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus thermodenitrificans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-07-09 Released: 2018-12-19 
• Deposition Author(s): Yamaguchi, A., Tada, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.195 
• R-Value Work: 0.147 
• R-Value Observed: 0.149 

Literature

Structures of endo-1,5-alpha-L-arabinanase mutants from Bacillus thermodenitrificans TS-3 in complex with arabino-oligosaccharides.

Yamaguchi, A., Sogabe, Y., Fukuoka, S., Sakai, T., Tada, T.

(2018) Acta Crystallogr F Struct Biol Commun 74: 774-780

• PubMed: 30511671 
• DOI: 10.1107/S2053230X18015947
• Primary Citation of Related Structures:  
  6A8H, 6A8I


• PubMed Abstract: 
  

The thermostable endo-1,5-α-L-arabinanase from Bacillus thermodenitrificans TS-3 (ABN-TS) hydrolyzes the α-1,5-L-arabinofuranoside linkages of arabinan. In this study, the crystal structures of inactive ABN-TS mutants, D27A and D147N, were determined in complex with arabino-oligosaccharides. The crystal structures revealed that ABN-TS has at least six subsites in the deep V-shaped cleft formed across one face of the propeller structure. The structural features indicate that substrate recognition is profoundly influenced by the remote subsites as well as by the subsites surrounding the active center. The `open' structure of the substrate-binding cleft of the endo-acting ABN-TS is suitable for the random binding of several sugar units in polymeric substrates.

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Organizational Affiliation: 

Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
endo-alpha-(1->5)-L-arabinanase	A	321	Geobacillus thermodenitrificans	Mutation(s): 1  Gene Names: abn-ts EC: 3.2.1.99
Find proteins for Q93HT9 (Geobacillus thermodenitrificans) Explore Q93HT9  Go to UniProtKB:  Q93HT9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose	B, C	3		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.195 
• R-Value Work: 0.147 
• R-Value Observed: 0.149 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.125	α = 90
b = 77.032	β = 90
c = 88.701	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-07-09 
• Released Date: 2018-12-19 
Deposition Author(s): Yamaguchi, A., Tada, T.

Revision History  

• Version 1.0: 2018-12-19
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary