1W0N

Structure of uncomplexed Carbohydrate Binding Domain CBM36


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.8 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.129 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1016/j.str.2004.04.022
  • Primary Citation of Related Structures:  

  • 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 refi ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-1,4-BETA-XYLANASE D
A
131Paenibacillus polymyxaMutation(s): 0 
Gene Names: xynD
EC: 3.2.1.55
Find proteins for P45796 (Paenibacillus polymyxa)
Go to UniProtKB:  P45796
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.8 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.129 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 30.529α = 90.00
b = 40.187β = 90.00
c = 81.200γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-05-08
    Type: Data collection, Experimental preparation, Other