2PLQ

Crystal structure of the amidase from geobacillus pallidus RAPc8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing.

Agarkar, V.B.Kimani, S.W.Cowan, D.A.Sayed, M.F.Sewell, B.T.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 1174-1178

  • DOI: 10.1107/S1744309106043855
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase enzyme superfamily. It converts amides to the corresponding acids and ammonia and has application as an industrial catalyst. RAPc8 amidase has been clon ...

    The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase enzyme superfamily. It converts amides to the corresponding acids and ammonia and has application as an industrial catalyst. RAPc8 amidase has been cloned and functionally expressed in Escherichia coli and has been purified by heat treatment and a number of chromatographic steps. The enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 1.2 M sodium citrate, 400 mM NaCl, 100 mM sodium acetate pH 5.6 were selected for X-ray diffraction studies. A data set having acceptable statistics to 1.96 A resolution was collected under cryoconditions using an in-house X-ray source. The space group was determined to be primitive cubic P4(2)32, with unit-cell parameter a = 130.49 (+/-0.05) A. The structure was solved by molecular replacement using the backbone of the hypothetical protein PH0642 from Pyrococcus horikoshii (PDB code 1j31) with all non-identical side chains substituted with alanine as a probe. There is one subunit per asymmetric unit. The subunits are packed as trimers of dimers with D3 point-group symmetry around the threefold axis in such a way that the dimer interface seen in the homologues is preserved.


    Related Citations: 
    • The Crystal Structure of an aliphatic amidase from Geobacillus pallidus RAPc8
      Kimani, S.W.
      (2007) Thesis --: 1
    • The Crystal Structure of an aliphatic amidase from Geobacillus pallidus RAPc8
      () To be published --: --

    Organizational Affiliation

    Advanced Research Centre for Applied Microbiology, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aliphatic amidaseA348Aeribacillus pallidusMutation(s): 0 
Gene Names: amiEami
EC: 3.5.1.4
Find proteins for Q9L543 (Bacillus sp)
Explore Q9L543 
Go to UniProtKB:  Q9L543
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: P 42 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.398α = 90
b = 130.398β = 90
c = 130.398γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
PHASERphasing
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description