3HG8 | pdb_00003hg8

Crystal Structure of 5-SMe Derivatized DNA

• PDB DOI: https://doi.org/10.2210/pdb3HG8/pdb
• NAKB: 3HG8

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


• Deposited: 2009-05-13 Released: 2009-07-21 
• Deposition Author(s): Sheng, J., Hassan, A.E.A., Zhang, W., Huang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.192 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate

Fang, Z., Dantsu, Y., Chen, C., Zhang, W., Huang, Z.

(2023) ChemistrySelect 8

• DOI: https://doi.org/10.1002/slct.202302253

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 2.54 kDa 
• Atom Count: 201 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*(UMS)P*GP*(US2)P*AP*CP*AP*C)-3'	A	8	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free:  0.192 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.882	α = 90
b = 42.882	β = 90
c = 23.687	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-21 
Deposition Author(s): Sheng, J., Hassan, A.E.A., Zhang, W., Huang, Z.

Revision History  

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.5: 2023-08-02
  Changes: Database references, Derived calculations, Source and taxonomy
• Version 1.6: 2024-05-22
  Changes: Data collection