1V0N

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.124 
  • R-Value Work: 0.103 
  • R-Value Observed: 0.104 

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This is version 2.0 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:  
    1V0M, 1V0L, 1V0K, 1V0N

  • 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 deoxynojirimycin analogue, suggest unusual pK(a) changes of the enzyme's catalytic machinery upon binding ...

    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
UniProt
Find proteins for P26514 (Streptomyces lividans)
Explore P26514 
Go to UniProtKB:  P26514
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XYP
Query on XYP

Download Ideal Coordinates CCD File 
E [auth A]beta-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
XIF
Query on XIF

Download Ideal Coordinates CCD File 
D [auth A]PIPERIDINE-3,4-DIOL
C5 H11 N O2
IZXWMVPZODQBRB-RFZPGFLSSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
F [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.124 
  • R-Value Work: 0.103 
  • R-Value Observed: 0.104 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.328α = 90
b = 46.132β = 90
c = 86.382γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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