1V0M

Xylanase Xyn10a from Streptomyces lividans in complex with xylobio-deoxynojirimycin at pH 7.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.098 
  • R-Value Observed: 0.099 

wwPDB Validation 3D Report Full Report



Literature

Atomic Resolution Analyses of the Binding of Xylobiose-Derived Deoxynojirimycin and Isofagomine to Xylanase Xyn10A

Gloster, T.M.Williams, S.J.Roberts, S.Tarling, C.A.Wicki, J.Withers, S.G.Davies, G.J.

(2004) Chem Commun (Camb) 16: 1794

  • DOI: 10.1039/b405152a
  • Primary Citation of Related Structures:  
    1V0N, 1V0M, 1V0L, 1V0K

  • PubMed Abstract: 
  • The atomic resolution structures of xylobiose-derived isofagomine and xylobiose-derived deoxynojirimycin in complex with the xylanase Xyn10A from Streptomyces lividans reveal undistorted (4)C(1) chair conformed sugars and, in the case of the deoxynoj ...

    The atomic resolution structures of xylobiose-derived isofagomine and xylobiose-derived deoxynojirimycin in complex with the xylanase Xyn10A from Streptomyces lividans reveal undistorted (4)C(1) chair conformed sugars and, in the case of the deoxynojirimycin analogue, suggest unusual pK(a) changes of the enzyme's catalytic machinery upon binding.


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDO-1,4-BETA-XYLANASE AA313Streptomyces lividansMutation(s): 0 
Gene Names: xlnA
EC: 3.2.1.8
Find proteins for P26514 (Streptomyces lividans)
Explore P26514 
Go to UniProtKB:  P26514
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XYP
Query on XYP

Download CCD File 
A
beta-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
XDN
Query on XDN

Download CCD File 
A
PIPERIDINE-3,4,5-TRIOL
C5 H11 N O3
RMCNETIHECSPMZ-SCDXWVJYSA-N
 Ligand Interaction
IMD
Query on IMD

Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.098 
  • R-Value Observed: 0.099 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.884α = 90
b = 46.081β = 90
c = 85.789γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-16
    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: Atomic model, Data collection, Derived calculations, Other, Structure summary