5HP6 | pdb_00005hp6

Structure of AbnA, a GH43 extracellular arabinanase from Geobacillus stearothermophilus (a new conformational state)

• PDB DOI: https://doi.org/10.2210/pdb5HP6/pdb

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


• Deposited: 2016-01-20 Released: 2017-02-01 
• Deposition Author(s): Lansky, S., Salama, R., Shwartstien, O., Shoham, Y., Shoham, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.253 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Structure of AbnA, a GH43 extracellular arabinanase from Geobacillus stearothermophilus (a new conformational state)

Lansky, S., Salama, R., 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.44 kDa 
• Atom Count: 6,573 
• Modeled Residue Count: 802 
• Deposited Residue Count: 848 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular arabinanase	A	848	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: abnA
UniProt
Find proteins for B3EYN2 (Geobacillus stearothermophilus) Explore B3EYN2  Go to UniProtKB:  B3EYN2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.253 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.847	α = 90
b = 82.641	β = 90
c = 132.069	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description