2EXK

Structure of the family43 beta-Xylosidase E187G from geobacillus stearothermophilus in complex with xylobiose

• PDB DOI: https://doi.org/10.2210/pdb2EXK/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-11-08 Released: 2006-04-04 
• Deposition Author(s): Brux, C., Niefind, K., Shallom-Shezifi, D., Shoham, Y., Schomburg, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.238 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 249.83 kDa 
• Atom Count: 18,715 
• Modelled Residue Count: 2,132 
• Deposited Residue Count: 2,140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-D-xylosidase	A, B, C, D	535	Geobacillus stearothermophilus	Mutation(s): 2  EC: 3.2.1.37
UniProt
Find proteins for Q09LX0 (Geobacillus stearothermophilus) Explore Q09LX0  Go to UniProtKB:  Q09LX0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose	E, F, G, H	2		N/A
Glycosylation Resources
GlyTouCan:  G92719DV GlyCosmos:  G92719DV

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	J [auth A], M [auth B], R [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	K [auth A], N [auth B], P [auth C], S [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	I [auth A], L [auth B], O [auth C], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.238 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.87	α = 90
b = 139.87	β = 90
c = 232.025	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-04 
Deposition Author(s): Brux, C., Niefind, K., Shallom-Shezifi, D., Shoham, Y., Schomburg, D.

Revision History  

• Version 1.0: 2006-04-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary
• Version 2.2: 2024-02-14
  Changes: Data collection