8TJ0 image
Deposition Date 2023-07-20
Release Date 2023-08-02
Last Version Date 2024-11-06
Entry Detail
PDB ID:
8TJ0
Title:
Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with 2 sticky base overhangs and 5' terminal phosphates and crosslinked with EDC.
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.24 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
I 2 2 2
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(A*CP*CP*CP*GP*GP*AP*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*AP*CP*GP*G)-3')
Chain IDs:A
Chain Length:32
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(A*GP*GP*CP*CP*GP*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*TP*CP*CP*G)-3')
Chain IDs:B
Chain Length:32
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Replication initiation protein
Gene (Uniprot):repE
Mutations:R118P
Chain IDs:C
Chain Length:263
Number of Molecules:1
Biological Source:Escherichia coli K-12
Primary Citation

Abstact

Biomolecular crystals can serve as materials for a plethora of applications including precise guest entrapment. However, as grown, biomolecular crystals are fragile in solutions other than their growth conditions. For crystals to achieve their full potential as hosts for other molecules, crystals can be made stronger with bioconjugation. Building on our previous work using carbodiimide 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide (EDC) for chemical ligation, here, we investigate DNA junction architecture through sticky base overhang lengths and the role of scaffold proteins in cross-linking within two classes of biomolecular crystals: cocrystals of DNA-binding proteins and pure DNA crystals. Both crystal classes contain DNA junctions where DNA strands stack up end-to-end. Ligation yields were studied as a function of sticky base overhang length and terminal phosphorylation status. The best ligation performance for both crystal classes was achieved with longer sticky overhangs and terminal 3'phosphates. Notably, EDC chemical ligation was achieved in crystals with pore sizes too small for intracrystal transport of ligase enzyme. Postassembly cross-linking produced dramatic stability improvements for both DNA crystals and cocrystals in water and blood serum. The results presented may help crystals containing DNA achieve broader application utility, including as structural biology scaffolds.

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Primary Citation of related structures