3GGK | pdb_00003ggk

Locating monovalent cations in one turn of G/C rich B-DNA

• PDB DOI: https://doi.org/10.2210/pdb3GGK/pdb
• NAKB: 3GGK

• Classification: DNA
• Mutation(s): No 


• Deposited: 2009-02-28 Released: 2010-03-09 
• Deposition Author(s): Maehigashi, T., Moulaei, T., Watkins, D., Komeda, S., Williams, L.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.87 Å
• R-Value Free: 
  0.134 (Depositor) 
• R-Value Work: 
  0.119 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.120 (Depositor) 

Starting Model: experimental

Literature

Locating monovalent cations in one turn of G/C rich B-DNA

Maehigashi, T., Moulaei, T., Watkins, D., Komeda, S., Williams, L.D.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 3.34 kDa 
• Atom Count: 453 
• Modeled Residue Count: 10 
• Deposited Residue Count: 10 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RB	G [auth A], H [auth A]	RUBIDIUM ION Rb NCCSSGKUIKYAJD-UHFFFAOYSA-N
MG	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.87 Å
• R-Value Free:  0.134 (Depositor) 
• R-Value Work:  0.119 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.120 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.135	α = 90
b = 25.156	β = 116.24
c = 34.113	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Maehigashi, T., Moulaei, T., Watkins, D., Komeda, S., Williams, L.D.

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description