4NC7: N-terminal Domain Of Delta-subunit Of Rna Polymerase Complexed With I3c And Nickel Ions

The crystal structure of the N-terminal domain of the RNA polymerase delta subunit (Ndelta) from Bacillus subtilis solved at a resolution of 2.0A is compared with the NMR structure determined previously. The molecule crystallizes in the space group C222(1) with a dimer in the asymmetric unit. Importantly, the X-ray structure exhibits significant differences from the lowest energy NMR structure. In addition to the overall structure differences, structurally important beta sheets found in the NMR structure are not present in the crystal structure. We systematically investigated the cause of the discrepancies between the NMR and X-ray structures of Ndelta, addressing the pH dependence, presence of metal ions, and crystal packing forces. We convincingly showed that the crystal packing forces, together with the presence of Ni(2+) ions, are the main reason for such a difference. In summary, the study illustrates that the two structural approaches may give unequal results, which need to be interpreted with care to obtain reliable structural information in terms of biological relevance.
PDB ID: 4NC7Download
MMDB ID: 121143
PDB Deposition Date: 2013/10/24
Updated in MMDB: 2014/08
Experimental Method:
x-ray diffraction
Resolution: 2  Å
Source Organism:
Similar Structures:
Biological Unit for 4NC7: dimeric; determined by author
Molecular Components in 4NC7
Label Count Molecule
Proteins (2 molecules)
DNA-directed RNA Polymerase Subunit Delta(Gene symbol: rpoE)
Molecule annotation
Chemicals (3 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB