3KSA

Detailed structural insight into the DNA cleavage complex of type IIA topoisomerases (cleaved form)

Structural Biology Knowledgebase: 3KSA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.176

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3KSA

Classification: ISOMERASE / DNA

Total Structure Weight: 194618.34


Macromolecule Entities
Molecule Chains Length Organism Details
DNA topoisomerase 4 subunit A A, B 496 Streptococcus pneumoniae EC#: 5.99.1.3 IUBMB
Fragment: residues 1-488
Gene Name(s): parC SP_0855
DNA topoisomerase 4 subunit B C, D 268 Streptococcus pneumoniae EC#: 5.99.1.3 IUBMB
Fragment: residues 404-647
Gene Name(s): parE SP_0852
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*AP*CP*CP*AP*AP*GP*GP*T*CP*AP*TP*GP*AP*AP*T)-3' E 15 synthetic E-site
5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3' F 19 synthetic E-site
5'-D(*CP*TP*GP*TP*TP*TP*TP*A*CP*GP*TP*GP*CP*AP*T)-3' G 15 synthetic E-site
5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3' H 19 synthetic E-site

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MG
Query on MG

C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.176
  • Space Group: P 32
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 116.91 α = 90.00
b = 116.91 β = 90.00
c = 183.76 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-11-21
  • Released Date: 2010-05-05
  • Deposition author(s): Laponogov, I., Pan, X.-S., Veselkov, D.A., McAuley, K.E., Fisher, L.M., Sanderson, M.R.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4