5E36 | pdb_00005e36

Crystal structure of 2'-propargyl-modified DNA 8mer-duplex

• PDB DOI: https://doi.org/10.2210/pdb5E36/pdb
• NAKB: 5E36

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


• Deposited: 2015-10-02 Released: 2015-12-02 
• Deposition Author(s): Sheng, J., Gan, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.161 (Depositor), 0.153 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 2'-propargyl-modified DNA 8mer-duplex

Sheng, J., Gan, J.

To be published.

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 7.54 kDa 
• Atom Count: 704 
• 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(*GP*(OMU)P*GP*TP*(5JO)P*CP*AP*C)-3')	A, B, C	8	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.161 (Depositor), 0.153 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.032	α = 90
b = 55.526	β = 90
c = 75.695	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-02 
Deposition Author(s): Sheng, J., Gan, J.

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description