3PBX | pdb_00003pbx

Strontium bound to the sequence d(CCGGCGCCGG)

• PDB DOI: https://doi.org/10.2210/pdb3PBX/pdb
• NAKB: 3PBX

• Classification: DNA
• Mutation(s): No 


• Deposited: 2010-10-21 Released: 2011-02-02 
• Deposition Author(s): Naseer, A., Cardin, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.327 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Starting Model: experimental

Literature

Strontium bound to the sequence d(CCGGCGCCGG)

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: 6.2 kDa 
• Atom Count: 463 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA	A, B	10	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SR	C [auth B]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N
NA	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.327 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.89	α = 90
b = 25.001	β = 110.01
c = 37.044	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-02 
Deposition Author(s): Naseer, A., Cardin, C.J.

Revision History  

• Version 1.0: 2011-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Database references, Refinement description, Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description