5BWI

Crystallographic structure of a bacterial heparanase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history. 


Literature

Functional and structural characterization of a heparanase.

Bohlmann, L., Tredwell, G.D., Yu, X., Chang, C.W., Haselhorst, T., Winger, M., Dyason, J.C., Thomson, R.J., Tiralongo, J., Beacham, I.R., Blanchard, H., von Itzstein, M.

(2015) Nat Chem Biol 11: 955-957

  • DOI: https://doi.org/10.1038/nchembio.1956
  • Primary Citation of Related Structures:  
    5BWI

  • PubMed Abstract: 

    We report the structural and functional characterization of a novel heparanase (BpHep) from the invasive pathogenic bacterium Burkholderia pseudomallei (Bp), showing ∼24% sequence identity with human heparanase (hHep). Site-directed mutagenesis studies confirmed the active site resi-dues essential for activity, and we found that BpHep has specificity for heparan sulfate. Finally, we describe the first heparanase X-ray crystal structure, which provides new insight into both substrate recognition and inhibitor design.

    • Organizational Affiliation: 

    Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, Queensland, Australia.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside Hydrolase Family 79
A, B
446Burkholderia pseudomalleiMutation(s): 0 
Gene Names: DP46_278, DP55_3260
UniProt
Find proteins for Q63T97 (Burkholderia pseudomallei (strain K96243))
Explore Q63T97 
Go to UniProtKB:  Q63T97
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63T97
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.03α = 90
b = 125.03β = 90
c = 125.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-11
    Changes: Structure summary
  • Version 1.2: 2015-11-25
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary