7Z7W

REP-related Chom18 variant with double GC base pairing

Summary for 7Z7W

• Entry DOI: 10.2210/pdb7z7w/pdb
• Descriptor: Chom18-GC DNA, STRONTIUM ION (2 entities in total)
• Functional Keywords: mismatch, non-canonical, base pair, double helix, dna
• Biological source: Cardiobacterium hominis
• Total number of polymer chains: 1
• Total formula weight: 5607.16

Authors

Svoboda, J.,Schneider, B.,Berdar, D.,Kolenko, P. (deposition date: 2022-03-16, release date: 2023-03-29, Last modification date: 2024-02-07)

Primary citation

Svoboda, J.,Berdar, D.,Kolenko, P.,Cerny, J.,Novakova, Z.,Pavlicek, J.,Schneider, B.
Conformation-based refinement of 18-mer DNA structures.
Acta Crystallogr D Struct Biol, 79:655-665, 2023

PubMed Abstract: Nine new crystal structures of CG-rich DNA 18-mers with the sequence 5'-GGTGGGGGC-XZ-GCCCCACC-3', which are related to the bacterial repetitive extragenic palindromes, are reported. 18-mer oligonucleotides with the central XZ dinucleotide systematically mutated to all 16 sequences show complex behavior in solution, but all ten so far successfully crystallized 18-mers crystallized as A-form duplexes. The refinement protocol benefited from the recurrent use of geometries of the dinucleotide conformer (NtC) classes as refinement restraints in regions of poor electron density. The restraints are automatically generated at the dnatco.datmos.org web service and are available for download. This NtC-driven protocol significantly helped to stabilize the structure refinement. The NtC-driven refinement protocol can be adapted to other low-resolution data such as cryo-EM maps. To test the quality of the final structural models, a novel validation method based on comparison of the electron density and conformational similarity to the NtC classes was employed.

PubMed: 37338420
DOI: 10.1107/S2059798323004679

Experimental method

X-RAY DIFFRACTION (2.75 Å)