1QTO

1.5 A CRYSTAL STRUCTURE OF A BLEOMYCIN RESISTANCE DETERMINANT FROM BLEOMYCIN-PRODUCING STREPTOMYCES VERTICILLUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The 1.5 A crystal structure of a bleomycin resistance determinant from bleomycin-producing Streptomyces verticillus.

Kawano, Y.Kumagai, T.Muta, K.Matoba, Y.Davies, J.Sugiyama, M.

(2000) J Mol Biol 295: 915-925

  • DOI: 10.1006/jmbi.1999.3404
  • Primary Citation of Related Structures:  
    1QTO

  • PubMed Abstract: 
  • Bleomycin (Bm)-binding protein, designated BLMA, which is a Bm resistance determinant from Bm-producing Streptomyces verticillus, was crystallized in a form suitable for X-ray diffraction analysis. The diffraction intensity data were collected up to ...

    Bleomycin (Bm)-binding protein, designated BLMA, which is a Bm resistance determinant from Bm-producing Streptomyces verticillus, was crystallized in a form suitable for X-ray diffraction analysis. The diffraction intensity data were collected up to a resolution of 1.5 A with a merging R-value of 0.054 at a completeness of 94 %. The BLMA structure, determined by the single isomorphous replacement method including the anomalous scattering effect (SIR-AS) at a resolution of 2.0 A, was refined at 1.5 A resolution. The final R-factor was 19.0 % and R(free) was 22.1 % including 91 water molecules. The crystal packing showed a dimer form, which was generated by arm exchange. The 1.5 A high-resolution experiment allowed an analysis of the side-chain disorder of BLMA. The structural comparison of BLMA with a homologous protein from Streptoalloteichus hindustanus, designated Shble protein, showed that a Ser100-Gly103 loop was farther from the groove, which is a Bm-binding site, in BLMA than in the Shble protein. Furthermore the hydrophobicity of the groove in BLMA is much lower than that in the Shble protein. The structural differences between these proteins may be responsible for the observation that a half-saturating concentration (K(1/2)) of Bm is higher for BLMA than for the Shble protein.


    Related Citations: 
    • Characterisation by molecular cloning of two genes from Streptomyces verticillus encoding resistance to bleomycin
      Sugiyama, M., Thompson, C.J., Kumagai, T., Suzuki, K., Deblaere, R., Villarroel, R., Davies, J.
      (1994) Gene 151: 11
    • Overproduction of the bleomycin-binding proteins from bleomycin-producing Streptomyces verticillus and a methicillin-resistant Staphylococcus aureus in Escherichia coli and their immunological characterisation
      Sugiyama, M., Kumagai, T., Matsuo, H., Bhuiyan, M.Z.A., Ueda, K., Mochizuki, H., Nakamura, N., Davies, J.
      (1995) FEBS Lett 362: 80
    • Crystallization and preliminary X-ray diffraction studies of bleomycin-binding protein from bleomycin-producing Streptomyces verticillus
      Kumagai, T., Muta, K., Matoba, Y., Kawano, Y., Kamiya, N., Davies, J., Sugiyama, M.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 127
    • Characterization of the bleomycin resistance determinant encoded on the transposon Tn5
      Kumagai, T., Nakano, T., Maruyama, M., Mochizuki, H., Sugiyama, M.
      (1999) FEBS Lett 442: 34
    • Mutation of the N-terminal proline 9 of BLMA from Streptomyces verticillus abolishes the binding affinity for bleomycin
      Kumagai, T., Hibino, R., Kawano, Y., Sugiyama, M.
      (1999) FEBS Lett 450: 227

    Organizational Affiliation

    RIKEN Harima Institute, Mikazuki-cho, Sayo, Hyogo, 679-5143, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BLEOMYCIN-BINDING PROTEINA122Streptomyces verticillusMutation(s): 0 
Gene Names: ble
Find proteins for Q53793 (Streptomyces verticillus)
Explore Q53793 
Go to UniProtKB:  Q53793
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.94α = 90
b = 67.88β = 90
c = 35.61γ = 90
Software Package:
Software NamePurpose
DMmodel building
X-PLORrefinement
WEISdata reduction
CCP4data scaling
ROTAVATAdata scaling
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-06-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2017-10-04
    Changes: Refinement description