5HON | pdb_00005hon

Structure of Domain 4 of AbnA, a GH43 extracellular arabinanase from Geobacillus stearothermophilus, in complex with arabinotriose

• PDB DOI: https://doi.org/10.2210/pdb5HON/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-01-19 Released: 2017-02-01 
• Deposition Author(s): Lansky, S., Azoulai, D., Shwartstien, O., Shoham, Y., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.197 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Structure of Domain 4 of AbnA, a GH43 extracellular arabinanase from Geobacillus stearothermophilus, in complex with arabinotriose

Lansky, S., Azoulai, D., Shwartstien, O., Shoham, Y., Shoham, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 46.42 kDa 
• Atom Count: 3,633 
• Modeled Residue Count: 412 
• Deposited Residue Count: 418 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular arabinanase	A, B	209	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: abnA
UniProt
Find proteins for B3EYN2 (Geobacillus stearothermophilus) Explore B3EYN2  Go to UniProtKB:  B3EYN2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose	C, D	3		N/A
Glycosylation Resources
GlyTouCan:  G56809YT GlyCosmos:  G56809YT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.197 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.408	α = 90
b = 77.15	β = 106.68
c = 68.622	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Lansky, S., Azoulai, D., Shwartstien, O., Shoham, Y., Shoham, G.

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary