7B4Z | pdb_00007b4z

Synthetic DNA duplex dodecamer

• PDB DOI: https://doi.org/10.2210/pdb7B4Z/pdb
• NAKB: 7B4Z
• BMRB: 34579

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


• Deposited: 2020-12-03 Released: 2020-12-16 
• Deposition Author(s): Lomzov, A.A., Shernuykov, A.V., Sviridov, E.A., Shevelev, G.Y., Bagryanskaya, E.G., Pyshnyi, D.V.
• Funding Organization(s): Russian Science Foundation, Ministry of Education and Science of the Russian Federation

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: all calculated structures submitted 

Literature

Study of a DNA Duplex by Nuclear Magnetic Resonance and Molecular Dynamics Simulations. Validation of Pulsed Dipolar Electron Paramagnetic Resonance Distance Measurements Using Triarylmethyl-Based Spin Labels.

Lomzov, A.A., Sviridov, E.A., Shernuykov, A.V., Shevelev, G.Y., Pyshnyi, D.V., Bagryanskaya, E.G.

(2016) J Phys Chem B 120: 5125-5133

• DOI: https://doi.org/10.1021/acs.jpcb.6b03193

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 6.09 kDa 
• Atom Count: 404 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3')	A	10	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3')	B	10	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: all calculated structures submitted 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Lomzov, A.A., Shernuykov, A.V., Sviridov, E.A., Shevelev, G.Y., Bagryanskaya, E.G., Pyshnyi, D.V.

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Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	18-14-00357
Ministry of Education and Science of the Russian Federation	Russian Federation	A-0309-2016-0004

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Data collection, Database references