5NT5 | pdb_00005nt5

The effect of Berenil and Cacodylateon the crystal structure of d(CGTGAATTCACG)

• PDB DOI: https://doi.org/10.2210/pdb5NT5/pdb
• NAKB: 5NT5

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


• Deposited: 2017-04-27 Released: 2017-09-20 
• Deposition Author(s): Sbirkova, H.I., Shivachev, B.L.
• Funding Organization(s): NSFB

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.312 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

Literature

The effect of Berenil and Cacodylateon the crystal structure of d(CGTGAATTCACG)

Sbirkova, H.I., Shivachev, B.L.

To be published.

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 7.48 kDa 
• Atom Count: 507 
• 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
CAC	C [auth A]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.312 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.044	α = 90
b = 41.534	β = 90
c = 64.868	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-09-20 
Deposition Author(s): Sbirkova, H.I., Shivachev, B.L.

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Funding Organization	Location	Grant Number
NSFB	Bulgaria	T02/14

Revision History  

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Data collection, Source and taxonomy
• Version 1.2: 2019-10-16
  Changes: Data collection
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description