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HYDROXYNITRILE-LYASE FROM HEVEA BRASILIENSIS AT ATOMIC RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Also Cited By: 1SC9, 1SCI, 1SCK, 1SCQ, 3C6X, 3C6Y, 3C6Z, 3C70

  • 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 ...

    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: 
    • Crystallization of a Hydroxynitrile Lyase
      Wagner, U.G.,Schall, M.,Hayn, M.,Hasslacher, M.,Schwab, H.,Griengl, H.S.,Kratky, C.
      (1996) Acta Crystallogr.,Sect.D 52: 591
    • 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
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYDROXYNITRILE LYASE
A
257Hevea brasiliensisGene Names: HNL
EC: 4.1.2.47
Find proteins for P52704 (Hevea brasiliensis)
Go to UniProtKB:  P52704
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.144 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 47.287α = 90.00
b = 106.655β = 90.00
c = 128.160γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance