6A1O

Crystal structures of disordered Z-type helices

• PDB DOI: https://doi.org/10.2210/pdb6A1O/pdb
• NAKB: 6A1O

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


• Deposited: 2018-06-07 Released: 2019-01-16 
• Deposition Author(s): Karthik, S., Mandal, P.K., Thirugnanasambandam, A., Gautham, N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.299 
• R-Value Work: 0.280 
• R-Value Observed: 0.275 

Literature

Crystal structures of disordered Z-type helices.

Karthik, S., Mandal, P.K., Thirugnanasambandam, A., Gautham, N.

(2019) Nucleosides Nucleotides Nucleic Acids 38: 279-293

• PubMed: 30588873 
• DOI: https://doi.org/10.1080/15257770.2018.1517883
• Primary Citation of Related Structures:  
  6A1O, 6A1Q


• PubMed Abstract: 
  

  The X-ray crystal structures of a decamer sequence d(CGCGTACGCG) ₂ and a tetradecamer sequence d(CGCGCGTACGCGCG) ₂ are presented here. Both sequences are alternating pyrimidine-purine repeat sequences and they form disordered, pseudo-continuous left handed Z-type helices. They demonstrate interesting variants of the 'bundles of columns of helices' mode of packing.

---

Organizational Affiliation: 

a Centre of Advanced Study in Crystallography and Biophysics , University of Madras, Guindy Campus , Chennai , Tamil Nadu , India.

Biological Assembly 1  

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

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 3.53 kDa 
• Atom Count: 249 
• Modelled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*G)-3')	A	2	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*A)-3')	B	2	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*GP*TP*G)-3')	C	4	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*AP*CP*A)-3')	D	4	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.299 
• R-Value Work: 0.280 
• R-Value Observed: 0.275 
• Space Group: P 6₅
• Diffraction Data: https://doi.org/10.5281/zenodo.2546741

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.112	α = 90
b = 31.112	β = 90
c = 43.044	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Karthik, S., Mandal, P.K., Thirugnanasambandam, A., Gautham, N.

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2019-01-30
  Changes: Data collection, Database references
• Version 1.2: 2019-05-22
  Changes: Data collection, Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description