6A1Q

Crystal structures of disordered Z-type helices

• PDB DOI: https://doi.org/10.2210/pdb6A1Q/pdb
• NAKB: 6A1Q

• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.276 
• R-Value Work: 0.274 
• R-Value Observed: 0.271 

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.

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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)

Biological Assembly 3  

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 7.14 kDa 
• Atom Count: 493 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*GP*TP*G)-3')	A, C, E	4	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*AP*CP*A)-3')	B, D, F	4	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.276 
• R-Value Work: 0.274 
• R-Value Observed: 0.271 
• Space Group: P 3₂
• Diffraction Data: https://doi.org/10.5281/zenodo.2546760

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.675	α = 90
b = 30.675	β = 90
c = 42.355	γ = 120

Software Package:

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

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