1QJ4

HYDROXYNITRILE-LYASE FROM HEVEA BRASILIENSIS AT ATOMIC RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.144 
  • R-Value Observed: 0.115 

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This is version 1.4 of the entry. See complete history


Literature

Atomic Resolution Crystal Structure of Hydroxynitrile Lyase from Hevea Brasiliensis

Gruber, K.Gugganig, M.Wagner, U.G.Kratky, C.

(1999) Biol Chem 380: 993

  • DOI: 10.1515/BC.1999.123
  • Primary Citation of Related Structures:  
    1QJ4

  • PubMed Abstract: 
  • The X-ray crystal structure of native hydroxynitrile lyase from Hevea brasiliensis (Hb-HNL) has been determined at 1.1 A resolution. It refined to a final R of 11.5% for all data and an Rfree of 14.4%. The favorable data-to-parameter ratio at atomic resolution made the refinement of individual anisotropic displacement parameters possible ...

    The X-ray crystal structure of native hydroxynitrile lyase from Hevea brasiliensis (Hb-HNL) has been determined at 1.1 A resolution. It refined to a final R of 11.5% for all data and an Rfree of 14.4%. The favorable data-to-parameter ratio at atomic resolution made the refinement of individual anisotropic displacement parameters possible. The data also allowed a clear distinction of the alternate orientations of all histidine and the majority of asparagine and glutamine side chains. A number of hydrogen atoms, including one on the imidazole of the mechanistically important His-235, became visible as peaks in a difference electron density map. The structure revealed a discretely disordered sidechain of Ser-80, which is part of the putative catalytic triad. Analysis of the anisotropy indicated an increased mobility of residues near the entrance to the active site and within the active site.


    Related Citations: 
    • Three-Dimensional Structures of Enzyme-Substrate Complexes of the Hydroxynitrile Lyase from Hevea Brasiliensis
      Zuegg, J., Gruber, K., Gugganig, M., Wagner, U.G., Kratky, C.
      (2000) Protein Sci 8: 1990
    • Mechanism of Cyanogenesis: The Crystal Structure of Hydroxynitrile Lyase from Hevea Brasiliensis
      Wagner, U.G., Hasslacher, M., Griengl, H., Schwab, H., Kratky, C.
      (1996) Structure 4: 811
    • Crystallization of a Hydroxynitrile Lyase
      Wagner, U.G., Schall, M., Hayn, M., Hasslacher, M., Schwab, H., Griengl, H.S., Kratky, C.
      (1996) Acta Crystallogr D Biol Crystallogr 52: 591
    • Molecular Cloning of the Full-Length Cdna of (S)-Hydroxynitrile Lyase from Hevea Brasiliensis. Functional Expression in Escherichia Coli and Saccharomyces Cerevisiae and Identification of an Active Site Residue
      Hasslacher, M., Schall, M., Hayn, M., Griengl, H., Kohlwein, S.D., Schwab, H.
      (1996) J Biol Chem 271: 5884

    Organizational Affiliation

    Abteilung für Strukturbiologie, Institut für Physikalische Chemie, Universität Graz, Austria.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYDROXYNITRILE LYASEA257Hevea brasiliensisMutation(s): 0 
Gene Names: HNL
EC: 4.1.2.39 (PDB Primary Data), 4.1.2.47 (UniProt)
UniProt
Find proteins for P52704 (Hevea brasiliensis)
Explore P52704 
Go to UniProtKB:  P52704
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.144 
  • R-Value Observed: 0.115 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.287α = 90
b = 106.655β = 90
c = 128.16γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-10-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-22
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection