9N7J

Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C6-TTTT DNA conjugate at 3.12 Angstrom resolution

Summary for 9N7J

• Entry DOI: 10.2210/pdb9n7j/pdb
• Related: 9BWU 9N2U 9N33 9N34 9N53 9N56 9N57 9N5S 9N5W 9N60 9N6S 9N7C 9N7H 9N7I
• Descriptor: Glutarate 2-hydroxylase, FE (II) ION (3 entities in total)
• Functional Keywords: oxygenase, hydroxylase, metal binding, metal binding protein
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 74686.20

Authors

Han, Z.,Mirkin, C.A. (deposition date: 2025-02-05, release date: 2026-07-29, Last modification date: 2026-08-12)

Primary citation

Han, Z.,Mirkin, C.A.
Diffraction-quality, ultraflexible protein single crystals engineered with DNA.
Sci Adv, 12:eaeh2948-eaeh2948, 2026

PubMed Abstract: DNA-functionalized colloidal nanoparticles assemble through flexible, nanoscale DNA hybridization interactions that limit atomic-level structural order. Here, we report a valence-centric strategy that enables DNA-bonded, protein single crystals with unconventional mechanical properties. An octameric enzyme, glutarate L-2-hydroxylase, was site- and number-selectively conjugated with eight self-complementary single-stranded DNA, yielding octavalent molecular bonds. The resulting conjugate assembled into the designed body-centered tetragonal crystals that diffracted to 1.42- to 2.61-angstrom resolution, with contacts mediated by B-form DNA helices spanning 17 to 25 angstroms. Increasing oligonucleotide length induces anisotropic lattice expansion while preserving atomic periodicity, even with partial DNA occupancy. Mechanistic studies suggest that the dynamic motion of unhybridized DNA facilitates crystallization, analogous to fluctuating electron clouds in atomic bonding. Compared with native protein crystals, DNA-hybridized crystals are 23-fold softer. These results challenge the assumption that flexibility is incompatible with structural order and establish a programmable framework for biomolecular crystallization and nanomaterials engineering with atomic precision.

PubMed: 42525757
DOI: 10.1126/sciadv.aeh2948

Experimental method

X-RAY DIFFRACTION (3.121 Å)