4I3H

A three-gate structure of topoisomerase IV from Streptococcus pneumoniae

Structural Biology Knowledgebase: 4I3H SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.185

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4I3H

Classification: ISOMERASE / DNA

Total Structure Weight: 298558.32


Macromolecule Entities
Molecule Chains Length Organism Details
Topoisomerase IV subunit B, DNA topoisomerase 4 subunit A chimera A, B 1144 Streptococcus pneumoniae EC#: 5.99.1 IUBMB 5.99.1.3 IUBMB
Gene Name(s): parC HMPREF0837_11636 parE parE_1 parE_2 ERS013931_01942 ERS019163_01202 ERS019291_00674 ERS020121_01920 ERS020135_01913 ERS020141_01769 ERS020145_01936 ERS020146_02047 ERS020148_02032 ERS020155_02101 ERS020337_02089 ERS020491_01644 ERS020500_02044 ERS020520_01939 ERS020539_02044 ERS020644_02038 ERS020692_01365 ERS020728_02106 ERS020747_02075 ERS020755_02106 ERS020762_02053 ERS020808_01002 ERS020822_04226 ERS020901_02122 ERS020969_02060 ERS021056_02016 ERS021300_01930 ERS021354_07390 ERS021374_02134 ERS021449_01450 ERS021536_02104 ERS021551_02044 ERS021560_02480 ERS021634_06660 ERS021718_02180 ERS021862_02106 ERS021948_02079 ERS022016_02053 ERS022045_05659 ERS022051_00573 ERS022077_02120 ERS022165_02021 ERS022179_02017 ERS022246_02176 ERS022282_02163 ERS022329_02027 ERS022356_00661 ERS022373_02093 ERS022629_02079 ERS022641_02107 ERS036307_02129 ERS043844_01009 ERS043879_00489 ERS043989_00886 ERS068727_02048 ERS069276_02058 ERS069380_00646 ERS069939_00794 ERS070055_00784 ERS077210_02210 ERS077235_02181 ERS077238_02195 ERS077244_02138 ERS077257_02175 ERS077274_02209 ERS077289_02164 ERS077296_02129 ERS232471_01998 ERS232474_02100 ERS232499_02043 ERS232512_01799 ERS232514_02009 ERS445053_01875
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*AP*AP*AP*GP*GP*CP*GP*GP*TP*AP*AP*TP*AP*CP*GP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*AP*AP*TP*CP*AP*GP*G)-3') E, G 34 synthetic V-site DNA
DNA (5'-D(*CP*CP*TP*GP*AP*TP*TP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*CP*GP*TP*AP*TP*TP*AP*CP*CP*GP*CP*CP*TP*TP*TP*G)-3') F, H 34 synthetic V-site DNA

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

A, B, H MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.185
  • Space Group: P 42 21 2

Unit Cell:

Length (Å) Angle (°)
a = 160.60 α = 90.00
b = 160.60 β = 90.00
c = 280.56 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-26
  • Released Date: 2013-08-28
  • Deposition author(s): Laponogov, I., Veselkov, D.A., Pan, X.-S., Crevel, I., Fisher, L.M., Sanderson, M.R.

Revision History

  • 2013-12-04
    Type: Citation | Details: Citation update
  • 2013-09-04
    Type: Citation | Details: Citation update