3RAF | pdb_00003raf

Quinazolinedione-DNA cleavage complex of type IV topoisomerase from S. pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb3RAF/pdb
• NAKB: 3RAF

• Classification: ISOMERASE/DNA/ANTIBIOTIC
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-28 Released: 2012-03-28 
• Deposition Author(s): Laponogov, I., Pan, X.-S., Veselkov, D.A., McAuley, K.E., Fisher, L.M., Sanderson, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free: 
  0.206 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Inhibitor-stabilised cleavage complexes of topoisomerase IIa: structural analysis of drug-dependent inter- and intramolecular interactions

Laponogov, I., Pan, X.-S., Veselkov, D.A., McAuley, K.E., Fisher, L.M., Sanderson, M.R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content 

• Total Structure Weight: 185.5 kDa 
• Atom Count: 11,229 
• Modeled Residue Count: 1,418 
• Deposited Residue Count: 1,564 
• Unique protein chains: 2
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 4 subunit A	A, B	496	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: ParC EC: 5.99.1 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore P72525  Go to UniProtKB:  P72525

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 4 subunit B	C, D	268	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: ParE EC: 5.99.1 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q59961  Go to UniProtKB:  Q59961

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*CP*AP*TP*GP*AP*AP*T)-3'	E	7	N/A

Entity ID: 4
Molecule	Chains	Length	Organism	Image
5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*G)-3'	F	11	N/A

Entity ID: 5
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*TP*GP*CP*AP*T)-3'	G	7	N/A

Entity ID: 6
Molecule	Chains	Length	Organism	Image
5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*G)-3'	H	11	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PDQ	M [auth F], N [auth H]	3-amino-7-{(3R)-3-[(1S)-1-aminoethyl]pyrrolidin-1-yl}-1-cyclopropyl-6-fluoro-8-methylquinazoline-2,4(1H,3H)-dione C18 H24 F N5 O2 SMONLCFJGCJROJ-WDEREUQCSA-N
MG	I [auth A], J [auth B], K [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free:  0.206 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.55	α = 90
b = 158.55	β = 90
c = 210.33	γ = 120

Software Package:

Software Name	Purpose
GDE	data collection
PHASER	phasing
PHENIX	refinement
xia2	data reduction
xia2	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-28 
Deposition Author(s): Laponogov, I., Pan, X.-S., Veselkov, D.A., McAuley, K.E., Fisher, L.M., Sanderson, M.R.

Revision History  

• Version 1.0: 2012-03-28
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary