6F1G | pdb_00006f1g

The structure of AbnB-E201A, an intracellular 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus, in complex with arabinopentaose

• PDB DOI: https://doi.org/10.2210/pdb6F1G/pdb

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


• Deposited: 2017-11-21 Released: 2018-12-12 
• Deposition Author(s): Lansky, S., Shwartshtien, O., Salama, R., Shoham, Y., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

The structure of AbnB-E201A, an intracellular 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus, in complex with arabinopentaose

Lansky, S., Shwartshtien, O., Salama, R., Shoham, Y., Shoham, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.59 kDa 
• Atom Count: 2,898 
• Modeled Residue Count: 315 
• Deposited Residue Count: 315 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intracellular endo-alpha-(1->5)-L-arabinanase	A	315	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: abnB EC: 3.2.1.99
UniProt
Find proteins for B3EYM8 (Geobacillus stearothermophilus) Explore B3EYM8  Go to UniProtKB:  B3EYM8

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-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose	B	5		N/A
Glycosylation Resources
GlyTouCan:  G90034US GlyCosmos:  G90034US

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.96	α = 90
b = 89.21	β = 102.45
c = 40.839	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Lansky, S., Shwartshtien, O., Salama, R., Shoham, Y., Shoham, G.

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary