Results for the evaluation of the complex based on PDB Code: 3t72
Background
PDB Code 3t72 belongs to PhoB(E)-Sigma70(4)-(RNAP-Betha-flap-tip-helix)-DNA Transcription Activation Sub-Complex.
This complex is created by the union of two chains of the protein PhoB, one chain of RNA polymerase sigma factor rpoD, DNA-directed RNA polymerase subunit beta, and two DNA strands.
The formation of this complex, is required in order to manage the transcription of the genes that belongs to the phosphate regulon, which manages the phosphate (Makino K, et al.) which is one of the most sensible systems to regulate inorganic phosphorus in the cell.
Computational models are represented in brown color, while the crystallographic structure is shown in cyan.
Reconstruction of the Model by Structural Superimposition.
Comparison between the crystal structure of 3t72 (cyan) and the model obtained by superimposition based approach. (brown)
Animation showing the structural alignment between the crystal structure (cyan) and the superimposition-based approach model (brown)
The results obtained from structural superimposition are great, but a bit funny. Since the protein in anchored to one extreme of the DNA chain, when using superimposition and therefore, the rotation of the chain to put the protein in place, the DNA strand gets shifted to the other side, giving a correct result in the polypeptide chains, but a shifted one in the DNA strands.
The structural alignment was performed with Chimera USCF, giving an RMSD between 102 pruned atom pairs of 0.000 angstroms; (across all 102 pairs: 0.000)
Reconstruction of the Complex by using Modeller.
Comparison between the crystal structure of 3t72 (cyan) and the model obtained by Modeling-based approach. (brown)
Animation showing the structural alignment between the crystal structure (cyan) and the Modeling-based approach model (brown)
As we can see, our Modelled-based approach algorithm returns inadequate results. As happens also with Model: 4g83, it seems to perform incorrectly when the complex is based on homomeric chains.
The structural alignment was performed with Chimera USCF, and RMSD between 60 pruned atom pairs is 1.169 angstroms; (across all 102 pairs: 3.260)
