1V0L

Xylanase Xyn10A from Streptomyces lividans in complex with xylobio-isofagomine at pH 5.8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.118 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-1,4-BETA-XYLANASE A
A
313Streptomyces lividansMutation(s): 0 
Gene Names: xlnA
EC: 3.2.1.8
Find proteins for P26514 (Streptomyces lividans)
Go to UniProtKB:  P26514
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XYP
Query on XYP

Download SDF File 
Download CCD File 
A
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
XIF
Query on XIF

Download SDF File 
Download CCD File 
A
PIPERIDINE-3,4-DIOL
XYLOSE-DERIVED ISOFAGOMINE
C5 H11 N O2
IZXWMVPZODQBRB-RFZPGFLSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.118 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.018α = 90.00
b = 46.098β = 90.00
c = 86.254γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-16
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance