2B46

Crystal structure of an engineered uninhibited Bacillus subtilis xylanase in substrate bound state

• PDB DOI: https://doi.org/10.2210/pdb2B46/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-09-22 Released: 2006-09-19 
• Deposition Author(s): Sansen, S., Dewilde, M., De Ranter, C.J., Sorensen, J.F., Sibbesen, O., Gebruers, K., Brijs, K., Courtin, C.M., Delcour, J.A., Rabijns, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.198 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.67 kDa 
• Atom Count: 1,541 
• Modelled Residue Count: 185 
• Deposited Residue Count: 185 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase A	A [auth X]	185	Bacillus subtilis	Mutation(s): 2  Gene Names: xynA EC: 3.2.1.8
UniProt
Find proteins for P18429 (Bacillus subtilis (strain 168)) Explore P18429  Go to UniProtKB:  P18429

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	B [auth A]	2		N/A
Glycosylation Resources
GlyTouCan:  G87728WL GlyCosmos:  G87728WL

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900116	B [auth A]	4beta-beta-xylobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.198 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.653	α = 90
b = 60.653	β = 90
c = 95.513	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-19 
Deposition Author(s): Sansen, S., Dewilde, M., De Ranter, C.J., Sorensen, J.F., Sibbesen, O., Gebruers, K., Brijs, K., Courtin, C.M., Delcour, J.A., Rabijns, A.

Revision History  

• Version 1.0: 2006-09-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, 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, Derived calculations, Structure summary
• Version 2.2: 2024-02-14
  Changes: Data collection