5J5P

AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.174
  • R-Value Work: 0.150

Literature

Macromolecules
Sequence Display for 5J5P

Classification: ISOMERASE / DNA

Total Structure Weight: 98461.33


Macromolecule Entities
Molecule Chains Length Organism Details
DNA topoisomerase 4 subunit B A, B 409 Streptococcus pneumoniae EC#: 5.99.1.3 IUBMB
Fragment: ATPase N-terminal domain, residues 1-402
Mutation: N217D
Gene Name(s): parE SP_0852
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*CP*GP*CP*GP*C)-3') C, D, E, F 6 Synthetic construct

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

A, B PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.174
  • R-Value Work: 0.150
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 134.44 α = 90.00
b = 136.46 β = 90.00
c = 136.27 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2016-04-03
  • Released Date: 2017-07-26
  • Deposition author(s): Laponogov, I., Pan, X.-S., Skamrova, G., Umrekar, T., Fisher, L.M., Sanderson, M.R.

Revision History

No revisions since initial release