1MA8 | pdb_00001ma8

A-DNA decamer GCGTA(UMS)ACGC with incorporated 2'-methylseleno-uridine

• PDB DOI: https://doi.org/10.2210/pdb1MA8/pdb
• NAKB: 1MA8

• Classification: DNA
• Mutation(s): No 


• Deposited: 2002-08-01 Released: 2002-12-11 
• Deposition Author(s): Teplova, M., Wilds, C.J., Wawrzak, Z., Tereshko, V., Du, Q., Carrasco, N., Huang, Z., Egli, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.173 (Depositor) 
• R-Value Work: 
  0.149 (Depositor) 

Literature

Covalent incorporation of selenium into oligonucleotides for X-ray crystal structure determination via MAD: proof of principle

Teplova, M., Wilds, C.J., Wawrzak, Z., Tereshko, V., Du, Q., Carrasco, N., Huang, Z., Egli, M.

(2002) Biochimie 84: 849-858

• PubMed: 12458077 
• DOI: https://doi.org/10.1016/s0300-9084(02)01440-2
• Primary Citation Related Structures: 
  1MA8


• PubMed Abstract: 
  

  Selenium was incorporated into an oligodeoxynucleotide in the form of 2'-methylseleno-uridine (U(Se)). The X-ray crystal structure of the duplex left open bracket d(GCGTA)U(Se)d(ACGC) right open bracket (2) was determined by the multiwavelength anomalous dispersion (MAD) technique and refined to a resolution of 1.3 A, demonstrating that selenium can selectively substitute oxygen in DNA and that the resulting compounds are chemically stable. Since derivatization at the 2'-alpha-position with selenium does not affect the preference of the sugar for the C3'-endo conformation, this strategy is suitable for incorporating selenium into RNA. The availability of selenium-containing nucleic acids for crystallographic phasing offers an attractive alternative to the commonly used halogenated pyrimidines.

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Organizational Affiliation: 
• Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.25 kDa 
• Atom Count: 547 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*TP*AP*UMSP*AP*CP*GP*C)-3'	A, B	10	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.173 (Depositor) 
• R-Value Work:  0.149 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.555	α = 90
b = 43.967	β = 90
c = 45.34	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-11 
Deposition Author(s): Teplova, M., Wilds, C.J., Wawrzak, Z., Tereshko, V., Du, Q., Carrasco, N., Huang, Z., Egli, M.

Revision History  

• Version 1.0: 2002-12-11
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references