2PLQ

Crystal structure of the amidase from geobacillus pallidus RAPc8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.146 

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 62: 1174-1178

  • DOI: 10.1107/S1744309106043855

  • 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


    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 amidase
A
348Bacillus spMutation(s): 0 
Gene Names: amiE (ami)
EC: 3.5.1.4
Find proteins for Q9L543 (Bacillus sp)
Go to UniProtKB:  Q9L543
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.146 
  • Space Group: P 42 3 2
Unit Cell:
Length (Å)Angle (°)
a = 130.398α = 90.00
b = 130.398β = 90.00
c = 130.398γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
CrystalCleardata collection
PHENIXphasing
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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