Crystal structure of SeMet-HldC from Burkholderia pseudomallei

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 

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Expression and crystallographic studies of D-glycero-beta-D-manno-heptose-1-phosphate adenylyltransferase from Burkholderia pseudomallei

Park, J.Kim, H.Kim, S.Lee, D.Shin, D.H.

(2017) Acta Crystallogr F Struct Biol Commun 73: 90-94

  • DOI: https://doi.org/10.1107/S2053230X16020537
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The Gram-negative bacterium Burkholderia pseudomallei is the causative agent of melioidosis. D-glycero-β-D-manno-Heptose-1-phosphate adenylyltransferase (HldC) is the fourth enzyme of the ADP-L-glycero-β-D-manno-heptose biosynthesis pathway, which produces an essential carbohydrate comprising the inner core of lipopolysaccharide. Therefore, HldC is a potential target of antibiotics against melioidosis. In this study, HldC from B. pseudomallei has been cloned, expressed, purified and crystallized. Synchrotron X-ray data from a selenomethionine-substituted HldC crystal were also collected to 2.8 Å resolution. The crystal belonged to the primitive triclinic space group P1, with unit-cell parameters a = 74.0, b = 74.0, c = 74.9 Å, α = 108.4, β = 108.4, γ = 108.0°. Eight protomers are present in the unit cell and three out of five selenomethionines were found in each protomer using the PHENIX software suite. A full structural determination is in progress to elucidate the structure-function relationship of the protein.

  • Organizational Affiliation

    College of Pharmacy, Ewha W. University, 52 Ewhayeodae-gil, Seoul 03760, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative cytidylyltransferase
A, B, C, D, E
A, B, C, D, E, F, G, H
173Burkholderia pseudomallei K96243Mutation(s): 0 
Gene Names: BPSL0395
Find proteins for Q63XZ4 (Burkholderia pseudomallei (strain K96243))
Explore Q63XZ4 
Go to UniProtKB:  Q63XZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63XZ4
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.953α = 108.38
b = 73.953β = 108.38
c = 74.88γ = 108.02
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation of Korea (NRF) funded by the Ministry of EducationKorea, Republic Of2015R1D1A1A01058942

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-19
    Type: Initial release