3GNK | pdb_00003gnk

Calcium bound to the Holliday junction sequence d(TCGGCGCCGA)4

• PDB DOI: https://doi.org/10.2210/pdb3GNK/pdb
• NAKB: 3GNK

• Classification: DNA
• Mutation(s): No 


• Deposited: 2009-03-17 Released: 2009-03-31 
• Deposition Author(s): Naseer, A., Cardin, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.306 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Calcium bound to the Holliday junction sequence d(TCGGCGCCGA)4

Naseer, A., Cardin, C.J.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 12.31 kDa 
• Atom Count: 995 
• Modeled Residue Count: 40 
• Deposited Residue Count: 40 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	F [auth B], G [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.306 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.97	α = 90
b = 24.17	β = 110.37
c = 73.89	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data collection
CrysalisPro	data reduction
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-31 
Deposition Author(s): Naseer, A., Cardin, C.J.

Revision History  

• Version 1.0: 2009-03-31
  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: 2018-04-04
  Changes: Data collection
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description