1QJ4 | pdb_00001qj4

HYDROXYNITRILE-LYASE FROM HEVEA BRASILIENSIS AT ATOMIC RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 
    0.144 (Depositor), 0.135 (DCC) 
  • R-Value Work: 
    0.127 (DCC) 
  • R-Value Observed: 
    0.115 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 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: https://doi.org/10.1515/BC.1999.123
  • Primary Citation 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 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.


  • Organizational Affiliation
    • Abteilung für Strukturbiologie, Institut für Physikalische Chemie, Universität Graz, Austria.

Macromolecule Content 

  • Total Structure Weight: 29.74 kDa 
  • Atom Count: 2,725 
  • Modeled Residue Count: 256 
  • Deposited Residue Count: 257 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HYDROXYNITRILE LYASE257Hevea 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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52704
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free:  0.144 (Depositor), 0.135 (DCC) 
  • R-Value Work:  0.127 (DCC) 
  • R-Value Observed: 0.115 (Depositor) 
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
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description