6KFL | pdb_00006kfl

Crystal structure of a two-quartet DNA G-quadruplex complexed with the porphyrin TMPyP4

• PDB DOI: https://doi.org/10.2210/pdb6KFL/pdb
• NAKB: 6KFL

• Classification: DNA
• Organism(s): Pseudorabies virus Ea
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-08 Released: 2020-07-08 
• Deposition Author(s): Zhang, Y.S., Parkinson, G.N., Wei, D.G.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.262 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a two-quartet DNA G-quadruplex complexed with the porphyrin TMPyP4

Zhang, Y.S., Parkinson, G.N., Wei, D.G.

To be published.

Biological Assembly 1  

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 9.72 kDa 
• Atom Count: 739 
• Modeled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*CP*TP*CP*GP*GP*CP*GP*GP*CP*GP*GP*A)-3')	A, B	14	Pseudorabies virus Ea

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POH (Subject of Investigation/LOI)	G [auth A]	(1Z,4Z,9Z,15Z)-5,10,15,20-tetrakis(1-methylpyridin-1-ium-4-yl)-21,23-dihydroporphyrin C44 H38 N8 ABCGFHPGHXSVKI-LWQDQPMZSA-O
NCO (Subject of Investigation/LOI)	H [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
K (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.262 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.152	α = 90
b = 47.192	β = 113.15
c = 38.133	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Zhang, Y.S., Parkinson, G.N., Wei, D.G.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31672558

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description