Streptomyces lividans Xylan Binding Domain cbm13

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


High-resolution crystal structures of the lectin-like xylan binding domain from Streptomyces lividans xylanase 10A with bound substrates reveal a novel mode of xylan binding.

Notenboom, V.Boraston, A.B.Williams, S.J.Kilburn, D.G.Rose, D.R.

(2002) Biochemistry 41: 4246-4254

  • DOI: https://doi.org/10.1021/bi015865j
  • Primary Citation of Related Structures:  
    1KNL, 1KNM, 1MC9

  • PubMed Abstract: 

    Carbohydrate-binding module (CBM) family 13 includes the "R-type" or "ricin superfamily" beta-trefoil lectins. The C-terminal CBM, CBM13, of xylanase 10A from Streptomyces lividans is a family 13 CBM that is not only structurally similar to the "R-type" lectins but also somewhat functionally similar. The primary function of CBM13 is to bind the polysaccharide xylan, but it retains the ability of the R-type lectins to bind small sugars such as lactose and galactose. The association of CBM13 with xylan appears to involve cooperative and additive participation of three binding pockets in each of the three trefoil domains of CBM13, suggesting a novel mechanism of CBM-xylan interaction. Thus, the interaction of CBM13 with sugars displays considerable plasticity for which we provide a structural rationale. The high-resolution crystal structure of CBM13 was determined by multiple anomalous dispersion from a complex of CBM13 with a brominated ligand. Crystal structures of CBM13 in complex with lactose and xylopentaose revealed two distinct mechanisms of ligand binding. CBM13 has retained its specificity for lactose via Ricin-like binding in all of the three classic trefoil binding pockets. However, CBM13 has the ability to bind either the nonreducing galactosyl moiety or the reducing glucosyl moiety of lactose. The mode of xylopentaose binding suggests adaptive mutations in the trefoil sugar binding scaffold to accommodate internal binding on helical polymers of xylose.

  • Organizational Affiliation

    Protein Engineering Networks of Centres of Excellence and Department of Microbiology and Immunology and Biotechnology Laboratory, University of British Columbia, Vancouver, BC, Canada. valerie@nki.nl

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ENDO-1,4-BETA-XYLANASE A130Streptomyces lividansMutation(s): 0 
Gene Names: xlnA
Find proteins for P26514 (Streptomyces lividans)
Explore P26514 
Go to UniProtKB:  P26514
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26514
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.152 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.953α = 90
b = 55.953β = 90
c = 97.066γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance