8VH6 | pdb_00008vh6

[F:3Au+:F] Metal-mediated DNA base pair with 2-thio-thymidine in tensegrity triangle

  • Classification: DNA
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2023-12-31 Released: 2025-01-15 
  • Deposition Author(s): Vecchioni, S., Lu, B.
  • Funding Organization(s): Office of Naval Research (ONR), Department of Energy (DOE, United States), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.86 Å
  • R-Value Free: 
    0.182 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.150 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Metal-mediated 2-thio-thymidine DNA base pairs

Vecchioni, S.Lu, B.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*(2SV)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')21synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*CP*AP*(2SV)P*AP*CP*A)-3')7synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')7synthetic construct
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')7synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.86 Å
  • R-Value Free:  0.182 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.150 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.404α = 90
b = 107.404β = 90
c = 90.715γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Office of Naval Research (ONR)United StatesN000141912596
Department of Energy (DOE, United States)United StatesDE-SC0007991
National Science Foundation (NSF, United States)United States2106790
National Science Foundation (NSF, United States)United StatesCCF-2106790
National Science Foundation (NSF, United States)United StatesGCR-2317843

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release