3LLN | pdb_00003lln

Comparison between the orthorhombic an tetragonal form of the heptamer sequence d(GCG(xT)GCG)/d(CGCACGC).

• PDB DOI: https://doi.org/10.2210/pdb3LLN/pdb
• NAKB: 3LLN

• Classification: DNA
• Mutation(s): No 


• Deposited: 2010-01-29 Released: 2010-08-18 
• Deposition Author(s): Robeyns, K., Herdewijn, P., Van Meervelt, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Work: 
  0.226 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Comparison between the orthorhombic and tetragonal forms of the heptamer sequence d[GCG(xT)GCG]/d(CGCACGC)

Robeyns, K., Herdewijn, P., Van Meervelt, L.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1028-1031

• PubMed: 20823518 
• DOI: https://doi.org/10.1107/S1744309110031696
• Primary Citation of Related Structures:  
  3LLN


• PubMed Abstract: 
  

  Cyclohexene nucleic acid (CeNA) building blocks can be introduced into natural DNA sequences without a large conformational influence because of the ability of the six-membered sugar ring to mimic both the C2'-endo and C3'-endo conformations of the naturally occurring ribofuranose sugar ring. The non-self-complementary DNA sequence d[GCG(xT)GCG]/d(CGCACGC) with one incorporated CeNA (xT) moiety crystallizes in two forms: orthorhombic and tetragonal. The tetragonal form, which diffracts to 3 A resolution, is a kinetically stable polymorph of the orthorhombic form [Robeyns et al. (2010), Artificial DNA, 1, 1-7], which diffracts to 1.17 A resolution and is the thermodynamically stable form of the CeNA-incorporated duplex. Here, the two structures are compared, with special emphasis on the differences in crystal packing and the irreversible conversion of the kinetic form into the high-resolution diffracting thermodynamic form.

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Organizational Affiliation: 
• Department of Chemistry, Biomolecular Architecture and BioMacS, Katholieke Universiteit Leuven, Belgium.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 4.41 kDa 
• Atom Count: 298 
• Modeled Residue Count: 14 
• Deposited Residue Count: 14 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*GP*(XTR)P*GP*CP*G)-3')	A	7	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*AP*CP*GP*C)-3')	B	7	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	C [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Work:  0.226 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.482	α = 90
b = 25.482	β = 90
c = 81.147	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Robeyns, K., Herdewijn, P., Van Meervelt, L.

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description