1BGW

TOPOISOMERASE RESIDUES 410-1202,

• PDB DOI: https://doi.org/10.2210/pdb1BGW/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1996-02-20 Released: 1996-07-11 
• Deposition Author(s): Berger, J.M., Gamblin, S.J., Harrison, S.C., Wang, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.277 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 

Literature

Structure and mechanism of DNA topoisomerase II.

Berger, J.M., Gamblin, S.J., Harrison, S.C., Wang, J.C.

(1996) Nature 379: 225-232

• PubMed: 8538787 
• DOI: https://doi.org/10.1038/379225a0


• PubMed Abstract: 
  

  The crystal structure of a large fragment of yeast type II DNA topoisomerase reveals a heart-shaped dimeric protein with a large central hole. It provides a molecular model of the enzyme as an ATP-modulated clamp with two sets of jaws at opposite ends, connected by multiple joints. An enzyme with bound DNA can admit a second DNA duplex through one set of jaws, transport it through the cleaved first duplex, and expel it through the other set of jaws.

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Organizational Affiliation: 

Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 91.81 kDa 
• Atom Count: 5,666 
• Modelled Residue Count: 680 
• Deposited Residue Count: 793 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TOPOISOMERASE	A	793	Saccharomyces cerevisiae	Mutation(s): 0  EC: 5.6.2.2
UniProt
Find proteins for P06786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06786  Go to UniProtKB:  P06786

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.277 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.1	α = 90
b = 154.1	β = 90
c = 127.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-07-11 
Deposition Author(s): Berger, J.M., Gamblin, S.J., Harrison, S.C., Wang, J.C.

Revision History  

• Version 1.0: 1996-07-11
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Other, Structure summary