5IP8 | pdb_00005ip8

Lambda-Ru(TAP)2dppz bound to d(CCGGCTCCGG)

• PDB DOI: https://doi.org/10.2210/pdb5IP8/pdb
• NAKB: 5IP8

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2016-03-09 Released: 2017-03-29 
• Deposition Author(s): Souter, J.E., Hall, J.P., Cardin, C.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.220 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Sequence specific binding of light activated Ru-polypyridyls

Hall, J.P., Souter, J.E., Gurung, S.P., 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: 7.86 kDa 
• Atom Count: 577 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*GP*AP*GP*CP*CP*GP*G)-3')	A [auth B]	10	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*GP*CP*TP*CP*CP*GP*G)-3')	B [auth A]	10	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RKL	D [auth B], E [auth B]	Ru(tap)2(dppz) complex C38 H22 N12 Ru PIKVAZQLFXBUSD-UHFFFAOYSA-N
BA	C [auth B], F [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.220 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.45	α = 90
b = 47.45	β = 90
c = 35.13	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHELXDE	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Souter, J.E., Hall, J.P., Cardin, C.J.

---

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/K019279/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M004635/1

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Author supporting evidence
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations