2JCG

Apo form of the catabolite control protein A (ccpA) from bacillus megaterium, with the DNA binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the Apo Form of the Catabolite Control Protein a (Ccpa) from Bacillus Megaterium with a DNA-Binding Domain.

Singh, R.K.Palm, G.J.Panjikar, S.Hinrichs, W.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 253

  • DOI: 10.1107/S1744309107008949
  • Primary Citation of Related Structures:  
    2JCG

  • PubMed Abstract: 
  • Crystal structure determination of catabolite control protein A (CcpA) at 2.6 A resolution reveals for the first time the structure of a full-length apo-form LacI-GalR family repressor protein. In the crystal structures of these transcription regulators, the three-helix bundle of the DNA-binding domain has only been observed in cognate DNA complexes; it has not been observed in other crystal structures owing to its mobility ...

    Crystal structure determination of catabolite control protein A (CcpA) at 2.6 A resolution reveals for the first time the structure of a full-length apo-form LacI-GalR family repressor protein. In the crystal structures of these transcription regulators, the three-helix bundle of the DNA-binding domain has only been observed in cognate DNA complexes; it has not been observed in other crystal structures owing to its mobility. In the crystal packing of apo-CcpA, the protein-protein contacts between the N-terminal three-helix bundle and the core domain consisted of interactions between the homodimers that were similar to those between the corepressor protein HPr and the CcpA N-subdomain in the ternary DNA complex. In contrast to the DNA complex, the apo-CcpA structure reveals large subdomain movements in the core, resulting in a complete loss of contacts between the N-subdomains of the homodimer.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Analyses of Catabolite Control Protein A, Free and in Complex with its DNA-Binding Site
      Tebbe, J., Orth, P., Kuester-Schoeck, E., Hillen, W., Saenger, W., Hinrichs, W.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 67

    Organizational Affiliation

    Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOSE-RESISTANCE AMYLASE REGULATORA332Priestia megateriumMutation(s): 0 
Gene Names: ccpA
UniProt
Find proteins for P46828 (Bacillus megaterium)
Explore P46828 
Go to UniProtKB:  P46828
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.234 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.45α = 90
b = 74.45β = 90
c = 238.84γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection