2RGR Isomerase Dna date Oct 04, 2007
title Topoisomerase Iia Bound To G-Segment Dna
authors K.C.Dong, J.M.Berger
compound source
Molecule: Dna
Chain: C
Engineered: Yes
Synthetic: Yes

Molecule: Dna
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: Dna Topoisomerase 2
Chain: A
Fragment: Dna Binding And Cleavage Domain (Residues 419-117
Synonym: Dna Topoisomerase II
Ec: 5.99.1.3
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Top2, Tor3
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 4932
Expression_system_strain: Bcy123
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgal
symmetry Space Group: I 2 2 2
R_factor 0.229 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
85.435 126.801 223.492 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand MG enzyme Isomerase E.C.5.99.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for gate-DNA recognition and bending by type IIA topoisomerases., Dong KC, Berger JM, Nature. 2007 Dec 20;450(7173):1201-5. PMID:18097402
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (282 Kb) [Save to disk]
  • Biological Unit Coordinates (2rgr.pdb1.gz) 551 Kb
  • LPC: Ligand-Protein Contacts for 2RGR
  • CSU: Contacts of Structural Units for 2RGR
  • Likely Quarternary Molecular Structure file(s) for 2RGR
  • Structure Factors (200 Kb)
  • Retrieve 2RGR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2RGR from S2C, [Save to disk]
  • Re-refined 2rgr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2RGR 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 2RGR
  • 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 2RGR, from MSDmotif at EBI
  • Fold representative 2rgr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2rgr_C] [2rgr] [2rgr_D] [2rgr_A]
  • SWISS-PROT database: [P06786]
  • Domain organization of [TOP2_YEAST] by SWISSPFAM
  • Domains found in 2RGR: [TOP2c] [TOP4c ] by SMART
  • Other resources with information on 2RGR
  • Community annotation for 2RGR 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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