1NQ6

Crystal Structure of the catalytic domain of xylanase A from Streptomyces halstedii JM8

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

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This is version 1.3 of the entry. See complete history. 


Literature

Structure of xylanase Xys1delta from Streptomyces halstedii.

Canals, A., Vega, M.C., Gomis-Ruth, F.X., Diaz, M., Santamaria R, R.I., Coll, M.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1447-1453

  • DOI: https://doi.org/10.1107/s0907444903012629
  • Primary Citation of Related Structures:  
    1NQ6

  • PubMed Abstract: 

    Xylanases hydrolyze the beta-1,4-linked xylose backbone of xylans. They are of increasing interest in the paper and food industries for their pre-bleaching and bio-pulping applications. Such industries demand new xylanases to cover a wider range of cleavage specificity, activity and stability. The catalytic domain of xylanase Xys1 from Streptomyces halstedii JM8 was expressed, purified and crystallized and native data were collected to 1.78 A resolution with an R(merge) of 4.4%. The crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 34.05, b = 79.60, c = 87.80 A. The structure was solved by the molecular-replacement method using the structure of the homologue Xyl10A from Streptomyces lividans. In a similar manner to other members of its family, Xys1 folds to form a standard (beta/alpha)(8) barrel with the two catalytic functions, the acid/base and the nucleophile, at its C-terminal side. The overall structure is described and compared with those of related xylanases.

    • Organizational Affiliation: 

    Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Jordi Girona 18-26, 08034 Barcelona, Spain. acpcri@ibmb.csic.es


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xys1302Streptomyces halstediiMutation(s): 0 
Gene Names: xysA
EC: 3.2.1.8
UniProt
Find proteins for Q59922 (Streptomyces halstedii)
Explore Q59922 
Go to UniProtKB:  Q59922
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59922
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.05α = 90
b = 79.6β = 90
c = 87.8γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-21
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description