3KSB Isomerase Dna date Nov 21, 2009
title Detailed Structural Insight Into The Dna Cleavage Complex Of Topoisomerases (Re-Sealed Form)
authors I.Laponogov, X.S.Pan, D.A.Veselkov, K.E.Mcauley, L.M.Fisher, M.R.Sanderson
compound source
Molecule: Dna Topoisomerase 4 Subunit A
Chain: A, B
Fragment: Residues 1-488
Synonym: Parc55, Topoisomerase Iv Subunit A
Ec: 5.99.1.-
Engineered: Yes
Organism_scientific: Streptococcus Pneumoniae
Organism_taxid: 1313
Strain: 7785
Gene: Parc
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet29a

Molecule: Dna Topoisomerase 4 Subunit B
Chain: C, D
Fragment: Residues 404-647
Synonym: Pare30, Topoisomerase Iv Subunit B
Ec: 5.99.1.-
Engineered: Yes

Organism_scientific: Streptococcus Pneumoniae
Organism_taxid: 1313
Strain: 7785
Gene: Pare
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet19b

Molecule: 5'-D(Apcpcpapapgpgptcpaptpgpapaptp Tpaptpgpcpapcpgptpapapapapcpapg)-3';
Chain: E
Engineered: Yes
Other_details: E-Site

Synthetic: Yes

Molecule: 5'-D(Cptpgptptptptpacpgptpgpcpaptp Cpaptptpcpaptpgpapcpcptptpgpgpt)-3';
Chain: F
Engineered: Yes
Other_details: E-Site

Synthetic: Yes
symmetry Space Group: P 32
R_factor 0.181 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
116.757 116.757 182.811 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.50 Å
ligand MG enzyme Isomerase E.C.5.99.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


D, C


Primary referenceStructural basis of gate-DNA breakage and resealing by type II topoisomerases., Laponogov I, Pan XS, Veselkov DA, McAuley KE, Fisher LM, Sanderson MR, PLoS One. 2010 Jun 28;5(6):e11338. PMID:20596531
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (479 Kb) [Save to disk]
  • Biological Unit Coordinates (3ksb.pdb1.gz) 465 Kb
  • LPC: Ligand-Protein Contacts for 3KSB
  • CSU: Contacts of Structural Units for 3KSB
  • Structure Factors (265 Kb)
  • Retrieve 3KSB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KSB from S2C, [Save to disk]
  • Re-refined 3ksb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KSB 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 3KSB
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3KSB, from MSDmotif at EBI
  • Fold representative 3ksb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ksb] [3ksb_D] [3ksb_B] [3ksb_A] [3ksb_F] [3ksb_E] [3ksb_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3KSB: [TOP2c] [TOP4c ] by SMART
  • Other resources with information on 3KSB
  • Community annotation for 3KSB 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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