3IXN | pdb_00003ixn

Crystal structure of d(CCGGTACCGG) as B-DNA duplex

• PDB DOI: https://doi.org/10.2210/pdb3IXN/pdb
• NAKB: 3IXN

• Classification: DNA
• Mutation(s): No 


• Deposited: 2009-09-04 Released: 2010-09-15 
• Deposition Author(s): Venkadesh, S., Mandal, P.K., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free: 
  0.275 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.261 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.262 (Depositor) 

Starting Model: in silico

Literature

Crystal Structure of inverted repeat sequence d(CCGGTACCGG)as B-DNA duplex

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

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 6.27 kDa 
• Atom Count: 418 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')	A, B	10	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	C [auth A], D [auth B], E [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free:  0.275 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.261 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.262 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.94	α = 90
b = 32.94	β = 90
c = 94.854	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Venkadesh, S., Mandal, P.K., Gautham, N.

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-04-03
  Changes: Refinement description