5JU4 | pdb_00005ju4

Crystal structure of a DNA sequence d(CGTGAATTCACG) at 130K

• PDB DOI: https://doi.org/10.2210/pdb5JU4/pdb
• NAKB: 5JU4

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


• Deposited: 2016-05-10 Released: 2016-11-16 
• Deposition Author(s): Sbirkova, H., Schivachev, B.
• Funding Organization(s): NSFB

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.292 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a DNA sequence d(CGTGAATTCACG) at 130K

Sbirkova, H.I., Schivachev, B.L.

(2016) Bulg Chem Commun 48: 589-593

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 7.38 kDa 
• Atom Count: 544 
• 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*TP*GP*AP*AP*TP*TP*CP*AP*CP*G)-3')	A, B	12	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.292 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.503	α = 90
b = 41.09	β = 90
c = 65.184	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-11-16 
Deposition Author(s): Sbirkova, H., Schivachev, B.

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Funding Organization	Location	Grant Number
NSFB	Bulgaria	T0214

Revision History  

• Version 1.0: 2016-11-16
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description