2DZD

Crystal structure of the biotin carboxylase domain of pyruvate carboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the biotin carboxylase domain of pyruvate carboxylase from Bacillus thermodenitrificans

Kondo, S.Nakajima, Y.Sugio, S.Sueda, S.Islam, M.N.Kondo, H.

(2007) ACTA CRYSTALLOGR.,SECT.D 63: 885-890

  • DOI: 10.1107/S0907444907029423

  • PubMed Abstract: 
  • The biotin carboxylase (BC) domain of pyruvate carboxylase (PC) from Bacillus thermodenitrificans (BC-bPC) was crystallized in an orthorhombic form (space group P2(1)2(1)2(1)), with unit-cell parameters a = 79.6, b = 116.0, c = 115.7 A. Two BC protom ...

    The biotin carboxylase (BC) domain of pyruvate carboxylase (PC) from Bacillus thermodenitrificans (BC-bPC) was crystallized in an orthorhombic form (space group P2(1)2(1)2(1)), with unit-cell parameters a = 79.6, b = 116.0, c = 115.7 A. Two BC protomers are contained in the asymmetric unit. Diffraction data were collected at 100 K and the crystal structure was solved by the molecular-replacement method and refined against reflections in the 20.0-2.4 A resolution range, giving an R factor of 0.235 and a free R factor of 0.292. The overall structure of BC-bPC is similar to those of the BC subunits of Aquifex aeolicus PC (BC-aPC) and Escherichia coli ACC (BC-eACC). The crystal structure revealed that BC-bPC forms a unique dimeric quaternary structure, which might be caused as a result of the division of the BC domain from the rest of the protein. The position of domain B in BC-bPC differs from those in other enzymes of similar structure (BC-aPC and BC-eACC).


    Organizational Affiliation

    ZOEGENE Corporation, Aoba, Yokohama 227-8502, Japan. kondo@bio.kyutech.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
pyruvate carboxylase
A, B
461Geobacillus thermodenitrificansMutation(s): 0 
Gene Names: pycA
Find proteins for Q05FZ3 (Geobacillus thermodenitrificans)
Go to UniProtKB:  Q05FZ3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 79.609α = 90.00
b = 115.987β = 90.00
c = 115.729γ = 90.00
Software Package:
Software NamePurpose
EPMRphasing
HKL-2000data reduction
CNXrefinement
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-11
    Type: Refinement description