6X5D | pdb_00006x5d

Structure of Dickerson-Drew Dodecamer with 2'-MeSe-ara-T modification

• PDB DOI: https://doi.org/10.2210/pdb6X5D/pdb
• NAKB: 6X5D

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


• Deposited: 2020-05-25 Released: 2021-06-02 
• Deposition Author(s): Chen, C., Fang, Z., Huang, Z.
• Funding Organization(s): National Science Foundation (NSF, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

2'-Beta-Selenium Atom on Thymidine to Control Beta-Form DNA Conformation and Large Crystal Formation

Chen, C., Fang, Z., Huang, Z.

(2022) Cryst Growth Des 22: 3601-3604

• DOI: https://doi.org/10.1021/acs.cgd.2c00474

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 7.54 kDa 
• Atom Count: 620 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*(UWJ)P*CP*GP*CP*G)-3')	A, B	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.35	α = 90
b = 40.018	β = 90
c = 65.708	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-02 
Deposition Author(s): Chen, C., Fang, Z., Huang, Z.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History  

• Version 1.0: 2021-06-02
  Type: Initial release
  
• Version 1.1: 2022-12-28
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description