3R86 | pdb_00003r86

Crystal structure of d(CCGGTACCGG)2 as B-DNA duplex grown with 5 mM CoCl2

• PDB DOI: https://doi.org/10.2210/pdb3R86/pdb
• NAKB: 3R86

• Classification: DNA
• Mutation(s): No 


• Deposited: 2011-03-23 Released: 2011-04-06 
• Deposition Author(s): Venkadesh, S., Mandal, P.K., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.260 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.276 (Depositor) 

Starting Model: other

Literature

Crystal structure of d(CCGGTACCGG)2 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: 2.80 Å
• R-Value Free:  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.260 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.276 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.756	α = 90
b = 32.756	β = 90
c = 93.648	γ = 120

Software Package:

Software Name	Purpose
MxCuBE	data collection
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Venkadesh, S., Mandal, P.K., Gautham, N.

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-02-14
  Changes: Experimental preparation
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description