Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 13.27 kDa 
• Atom Count: 1079 
• Modelled Residue Count: 120 
• Deposited Residue Count: 120 
• Unique protein chains: 1

1UX7

Carbohydrate-Binding Module CBM36 in complex with calcium and xylotriose

• PDB DOI: 10.2210/pdb1UX7/pdb

• Classification: CARBOHYDRATE-BINDING MODULE
• Organism(s): Paenibacillus polymyxa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-02-19 Released: 2004-10-27 
• Deposition Author(s): Davies, G.J., Boraston, A.B., Jamal, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.202 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 

Literature

Ab Initio Structure Determination and Functional Characterization of Cbm36: A New Family of Calcium-Dependent Carbohydrate Binding Modules

Jamal, S., Boraston, A.B., Turkenburg, J.P., Tarbouriech, N., Ducros, V.M.-A., Davies, G.J.

(2004) Structure 12: 1177

• PubMed: 15242594 
• DOI: 10.1016/j.str.2004.04.022
• Primary Citation of Related Structures:  
  1UX7, 1W0N


• PubMed Abstract: 
  

The enzymatic degradation of polysaccharides harnesses multimodular enzymes whose carbohydrate binding modules (CBM) target the catalytic domain onto the recalcitrant substrate. Here we report the ab initio structure determination and subsequent refinement, at 0.8 A resolution, of the CBM36 domain of the Paenibacillus polymyxa xylanase 43A. Affinity electrophoresis, isothermal titration calorimetry, and UV difference spectroscopy demonstrate that CBM36 is a novel Ca(2+)-dependent xylan binding domain. The 3D structure of CBM36 in complex with xylotriose and Ca(2+), at 1.5 A resolution, displays significant conformational changes compared to the native structure and reveals the molecular basis for its unique Ca(2+)-dependent binding of xylooligosaccharides through coordination of the O2 and O3 hydroxyls. CBM36 is one of an emerging spectrum of carbohydrate binding modules that increasingly find applications in industry and display great potential for mapping the "glyco-architecture" of plant cells.

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Organizational Affiliation: 

Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDO-1,4-BETA-XYLANASE D	A	120	Paenibacillus polymyxa	Mutation(s): 0  Gene Names: xynD EC: 3.2.1.55
UniProt
Find proteins for P45796 (Paenibacillus polymyxa) Explore P45796  Go to UniProtKB:  P45796

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-1)-beta-D-xylopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G39164OL GlyCosmos:  G39164OL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.202 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.581	α = 90
b = 52.132	β = 90
c = 54.766	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-02-19 
• Released Date: 2004-10-27 
Deposition Author(s): Davies, G.J., Boraston, A.B., Jamal, S.

Revision History  

• Version 1.0: 2004-10-27
  Type: Initial release
  
• Version 1.1: 2011-05-07
  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: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary