4PUD

Extracellulr Xylanase from Geobacillus stearothermophilus: E159Q mutant, with xylopentaose in active site

• PDB DOI: https://doi.org/10.2210/pdb4PUD/pdb

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


• Deposited: 2014-03-13 Released: 2015-03-18 
• Deposition Author(s): Dann, R.D., Solomon, H.V., Lansky, S., Ben-David, A., Lavid, N., Salama, R., Shoham, Y., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.183 
• R-Value Work: 0.146 
• R-Value Observed: 0.148 

Literature

Extracellulr Xylanase from Geobacillus stearothermophilus: E159Q mutant, with xylopentaose in active site.

Dann, R.D., Solomon, H.V., Lansky, S., Ben-David, A., Lavid, N., Salama, R., 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: 44.37 kDa 
• Atom Count: 3,554 
• Modelled Residue Count: 371 
• Deposited Residue Count: 371 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase	A	371	Geobacillus stearothermophilus	Mutation(s): 1  EC: 3.2.1.8
UniProt
Find proteins for P40943 (Geobacillus stearothermophilus) Explore P40943  Go to UniProtKB:  P40943

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	B	5		N/A
Glycosylation Resources
GlyTouCan:  G47101GE GlyCosmos:  G47101GE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth A], M [auth A], N [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	E [auth A], F [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.183 
• R-Value Work: 0.146 
• R-Value Observed: 0.148 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.394	α = 90
b = 61.664	β = 119.37
c = 89.321	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
REFMAC	refinement
HKL-3000	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): Dann, R.D., Solomon, H.V., Lansky, S., Ben-David, A., Lavid, N., Salama, R., Shoham, Y., Shoham, G.

Revision History  

• Version 1.0: 2015-03-18
  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: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary