4O8O

Crystal structure of SthAraf62A, a GH62 family alpha-L-arabinofuranosidase from Streptomyces thermoviolaceus, bound to alpha-L-arabinose

• PDB DOI: https://doi.org/10.2210/pdb4O8O/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces thermoviolaceus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-12-28 Released: 2014-07-02 
• Deposition Author(s): Stogios, P.J., Wang, W., Xu, X., Cui, H., Master, E., Savchenko, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.156 
• R-Value Work: 0.139 
• R-Value Observed: 0.139 

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: 42.29 kDa 
• Atom Count: 2,957 
• Modelled Residue Count: 303 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-L-arabinofuranosidase	A	384	Streptomyces thermoviolaceus	Mutation(s): 0  Gene Names: stxIV
UniProt
Find proteins for Q76BV4 (Streptomyces thermoviolaceus) Explore Q76BV4  Go to UniProtKB:  Q76BV4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AHR	C [auth A]	alpha-L-arabinofuranose C5 H10 O5 HMFHBZSHGGEWLO-QMKXCQHVSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.156 
• R-Value Work: 0.139 
• R-Value Observed: 0.139 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.05	α = 90
b = 65.739	β = 90
c = 85.203	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-02 
Deposition Author(s): Stogios, P.J., Wang, W., Xu, X., Cui, H., Master, E., Savchenko, A.

Revision History  

• Version 1.0: 2014-07-02
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2022-08-24
  Changes: Database references, Structure summary