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Structure paper

TitleModular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds.
Journal, issue, pagesAcs Nano, Vol. 17, Page 13110-13120, Year 2023
Publish dateSep 29, 2021 (structure data deposition date)
AuthorsOrun, A.R. / Shields, E.T. / Dmytriw, S. / Vajapayajula, A. / Slaughter, C.K. / Snow, C.D.
External linksAcs Nano / PubMed:37407546
MethodsX-ray diffraction
Resolution2.38 - 3.3 Å
Structure data

PDB-7sdp:
Replication Initiator Protein REPE54 and cognate DNA sequence with terminal three prime phosphates.
Method: X-RAY DIFFRACTION / Resolution: 3.01 Å

PDB-7soz:
Replication Initiator Protein REPE54 and cognate DNA sequence with terminal three prime phosphates chemically crosslinked (5 mg/mL EDC, 12 hours).
Method: X-RAY DIFFRACTION / Resolution: 3.14 Å

PDB-7u6k:
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.
Method: X-RAY DIFFRACTION / Resolution: 2.38 Å

PDB-7u7o:
Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional T-A rich sequence.
Method: X-RAY DIFFRACTION / Resolution: 2.97 Å

PDB-7ufx:
Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and scaffold-insert duplexes (21mer and 10mer) containing the cognate REPE54 sequence and an additional G-C rich sequence, respectively.
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-7uog:
Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and asymmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence.
Method: X-RAY DIFFRACTION / Resolution: 2.63 Å

PDB-7ur0:
Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and scaffold-insert duplexes (21mer and 10mer) containing the cognate REPE54 sequence and an additional T-A rich sequence, respectively.
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-7uv6:
Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and scaffold duplex (21mer) containing the cognate REPE54 sequence and an insert duplex (10mer) with guest TAMRA-labelled thymine and G-C rich sequence.
Method: X-RAY DIFFRACTION / Resolution: 2.72 Å

PDB-7uv7:
Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and scaffold duplex (21mer) containing the cognate REPE54 sequence and an insert duplex (10mer) with guest TAMRA-labelled thymine and T-A rich sequence.
Method: X-RAY DIFFRACTION / Resolution: 3.02 Å

PDB-7uxy:
Isoreticular, interpenetrating co-crystal of protein variant Replication Initiator Protein REPE54 (L53G,Q54G,E55G) and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence.
Method: X-RAY DIFFRACTION / Resolution: 3.15 Å

PDB-8d86:
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 co-crystallized with a guest small molecule, netropsin.
Method: X-RAY DIFFRACTION / Resolution: 3.12 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-NT:
NETROPSIN / antibiotic, antivirus*YM

Source
  • escherichia coli (E. coli)
  • eschericia coli (E. coli)
  • escherichia coli k-12 (bacteria)
KeywordsDNA BINDING PROTEIN/DNA / Replication Initiator RepE Complex Co-Crystal / DNA BINDING PROTEIN-DNA complex / DNA BINDING PROTEIN

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