1CY9

CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. MONOCLINIC FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational changes in E. coli DNA topoisomerase I.

Feinberg, H.Lima, C.D.Mondragon, A.

(1999) Nat.Struct.Mol.Biol. 6: 918-922

  • DOI: 10.1038/13283
  • Primary Citation of Related Structures:  1CYY

  • PubMed Abstract: 
  • DNA topoisomerases are the enzymes responsible for maintaining the topological states of DNA. In order to change the topology of DNA, topoisomerases pass one or two DNA strands through transient single or double strand breaks in the DNA phosphodieste ...

    DNA topoisomerases are the enzymes responsible for maintaining the topological states of DNA. In order to change the topology of DNA, topoisomerases pass one or two DNA strands through transient single or double strand breaks in the DNA phosphodiester backbone. It has been proposed that both type IA and type II enzymes change conformation dramatically during the reaction cycle in order to accomplish these transformations. In the case of Escherichia coli DNA topoisomerase I, it has been suggested that a 30 kDa fragment moves away from the rest of the protein to create an entrance into the central hole in the protein. Structures of the 30 kDa fragment reveal that indeed this fragment can change conformation significantly. The fragment is composed of two domains, and while the domains themselves remain largely unchanged, their relative arrangement can change dramatically.


    Organizational Affiliation

    Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2153 Sheridan Road, Evanston, Illinois 60208, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA TOPOISOMERASE I
A, B
264Escherichia coli (strain K12)Gene Names: topA (supX)
EC: 5.99.1.2
Find proteins for P06612 (Escherichia coli (strain K12))
Go to UniProtKB:  P06612
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 36.820α = 90.00
b = 146.550β = 106.48
c = 64.570γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
DENZOdata reduction
X-PLORmodel building
AMoREphasing
REFMACrefinement
X-PLORrefinement
X-PLORphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance