2JCG | pdb_00002jcg

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 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 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: https://doi.org/10.1107/S1744309107008949
  • Primary Citation 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. 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.


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

Macromolecule Content 

  • Total Structure Weight: 36.71 kDa 
  • Atom Count: 2,469 
  • Modeled Residue Count: 322 
  • Deposited Residue Count: 332 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLUCOSE-RESISTANCE AMYLASE REGULATOR332Priestia megateriumMutation(s): 0 
UniProt
Find proteins for P46828 (Priestia megaterium)
Explore P46828 
Go to UniProtKB:  P46828
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46828
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.297 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
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

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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
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description