2VRQ

STRUCTURE OF AN INACTIVE MUTANT OF ARABINOFURANOSIDASE FROM THERMOBACILLUS XYLANILYTICUS IN COMPLEX WITH A PENTASACCHARIDE

• PDB DOI: https://doi.org/10.2210/pdb2VRQ/pdb

• Classification: HYDROLASE
• Organism(s): Thermobacillus xylanilyticus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-04-09 Released: 2008-07-01 
• Deposition Author(s): Paes, G., Skov, L.K., Odonohue, M.J., Remond, C., Kastrup, J.S., Gajhede, M., Mirza, O.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.201 
• R-Value Work: 0.182 
• R-Value Observed: 0.182 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 170.25 kDa 
• Atom Count: 13,062 
• Modelled Residue Count: 1,479 
• Deposited Residue Count: 1,488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-L-ARABINOFURANOSIDASE	A, B, C	496	Thermobacillus xylanilyticus	Mutation(s): 1  EC: 3.2.1.55
UniProt
Find proteins for O69262 (Thermobacillus xylanilyticus) Explore O69262  Go to UniProtKB:  O69262

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-arabinofuranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	D, E	4		N/A
Glycosylation Resources
GlyTouCan:  G78953UV GlyCosmos:  G78953UV

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-arabinofuranose-(1-3)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	F	3		N/A
Glycosylation Resources
GlyTouCan:  G96828DL GlyCosmos:  G96828DL

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], H [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.201 
• R-Value Work: 0.182 
• R-Value Observed: 0.182 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.8	α = 90
b = 156.8	β = 90
c = 378.6	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XIA-DPA	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-01 
Deposition Author(s): Paes, G., Skov, L.K., Odonohue, M.J., Remond, C., Kastrup, J.S., Gajhede, M., Mirza, O.

Revision History  

• Version 1.0: 2008-07-01
  Type: Initial release
  
• Version 1.1: 2011-05-12
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary