2Z33: Solution structure of the DNA complex of PhoB DNA-binding/transactivation Domain

The solution structure of the complex between the transcription factor PhoB DNA-binding/transactivation domain and DNA was determined by NMR spectroscopy and simulated annealing in a periodic boundary box of explicit water with the particle mesh Ewald method. The refined structures provided better convergence and better local geometry compared with the structures determined in vacuum. The hydrogen bond interactions between the PhoB domain and DNA in the aqueous environment were fully formed. The complex structure was found to be very similar to the crystal structure, particularly at the PhoB-DNA interface, much more so than expected from the vacuum structure. These results indicate the importance of the proper treatment of electrostatic and hydration influences in describing protein-DNA interactions. The hydration structures observed for the refined structures contained most of the crystal waters as a subset. We observed that various water-mediated PhoB-DNA interactions contributed to the molecular recognition between PhoB and DNA.
PDB ID: 2Z33Download
MMDB ID: 63957
PDB Deposition Date: 2007/5/31
Updated in MMDB: 2009/07
Experimental Method:
solution nmr
Source Organism:
Escherichia coli
Similar Structures:
Molecular Components in 2Z33
Label Count Molecule
Protein (1 molecule)
Phosphate Regulon Transcriptional Regulatory Protein Phob(Gene symbol: phoB)
Molecule annotation
Nucleotides(2 molecules)
Molecule annotation
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB