2O59 Isomerase Dna date Dec 05, 2006
title Structure Of E. Coli Topoisomerase III In Complex With An 8- Single Stranded Oligonucleotide. Frozen In Glycerol Ph 8.0
authors A.Changela, R.J.Digate, A.Mondragon
compound source
Molecule: 5'-D(Cpgpcpapapcptpt)-3'
Chain: C, D
Engineered: Yes
Synthetic: Yes

Molecule: Dna Topoisomerase 3
Chain: A, B
Synonym: Dna Topoisomerase III
Ec: 5.99.1.2
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Topb
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21
symmetry Space Group: P 43 21 2
R_factor 0.221 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
101.590 101.590 453.590 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand ACY, CL enzyme Isomerase E.C.5.99.1.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate., Changela A, Digate RJ, Mondragon A, J Mol Biol. 2007 Apr 20;368(1):105-18. Epub 2007 Feb 3. PMID:17331537
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (424 Kb) [Save to disk]
  • Biological Unit Coordinates (2o59.pdb1.gz) 211 Kb
  • Biological Unit Coordinates (2o59.pdb2.gz) 211 Kb
  • LPC: Ligand-Protein Contacts for 2O59
  • CSU: Contacts of Structural Units for 2O59
  • Likely Quarternary Molecular Structure file(s) for 2O59
  • Structure Factors (602 Kb)
  • Retrieve 2O59 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2O59 from S2C, [Save to disk]
  • Re-refined 2o59 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2O59 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2O59
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2O59, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2o59_C] [2o59] [2o59_B] [2o59_D] [2o59_A]
  • SWISS-PROT database: [P14294]
  • Domain organization of [TOP3_ECOLI] by SWISSPFAM
  • Domains found in 2O59: [TOP1Ac] [TOP1Bc] [TOPRIM ] by SMART
  • Other resources with information on 2O59
  • Community annotation for 2O59 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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