3V9D | pdb_00003v9d

Crystal structure of the tetra-decanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex

• PDB DOI: https://doi.org/10.2210/pdb3V9D/pdb
• NAKB: 3V9D

• Classification: DNA
• Mutation(s): No 


• Deposited: 2011-12-26 Released: 2012-04-18 
• Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: in silico

Literature

Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex

Mandal, P.K., Venkadesh, S., Gautham, N.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 393-399

• PubMed: 22505405 
• DOI: https://doi.org/10.1107/S174430911200869X
• Primary Citation Related Structures: 
  3V9D


• PubMed Abstract: 
  

  The crystal structure of the tetradecanucleotide sequence d(CCCCGGTACCGGGG)(2) has been determined at 2.5 Å resolution in the tetragonal space group P4(1). This sequence was designed with the expectation of a four-way junction. However, the sequence crystallized as an A-DNA duplex and represents more than one full turn of the A-helix. The crystallographic asymmetric unit consists of one tetradecanucleotide duplex. The structural parameters of the A-type DNA duplex structure and the crystal-packing arrangement are described. One Mn(2+) ion was identified with direct coordination to the N7 position of G(13) and a water molecule at the major-groove side of the C(2)·G(13) base pair.

---

Organizational Affiliation: 
• C. A. S. in Crystallography and Biophysics, University of Madras, Guindy, Chennai 600 025, India.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 8.62 kDa 
• Atom Count: 584 
• Modeled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*GP*G)-3')	A, B	14	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.34	α = 90
b = 29.34	β = 90
c = 87.687	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-18 
Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2014-03-12
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-04-03
  Changes: Refinement description