6K8O

Crystal structure of the Sulfolobus solfataricus topoisomerase III in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb6K8O/pdb
• NAKB: 6K8O

• Classification: ISOMERASE, DNA BINDING PROTEIN/DNA
• Organism(s): Saccharolobus solfataricus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-06-13 Released: 2020-06-24 
• Deposition Author(s): Wang, H.Q., Zhang, J.H., Zheng, X., Zheng, Z.F., Dong, Y.H., Huang, L., Gong, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.259 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 

Literature

Crystal structures of the Sulfolobus solfataricus topoisomerase III reveal that its C-terminal novel zinc finger part is a unique decatenation domain

Wang, H.Q., Zhang, J.H., Zheng, X., Zheng, Z.F., Dong, Y.H., Huang, L., Gong, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 79.19 kDa 
• Atom Count: 5,850 
• Modelled Residue Count: 673 
• Deposited Residue Count: 676 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
topoisomerase III	A	668	Saccharolobus solfataricus	Mutation(s): 1  EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
UniProt
Find proteins for Q97ZJ8 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97ZJ8  Go to UniProtKB:  Q97ZJ8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*AP*AP*GP*GP*TP*C)-3')	B	8	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.259 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.731	α = 90
b = 150.731	β = 90
c = 97.032	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Wang, H.Q., Zhang, J.H., Zheng, X., Zheng, Z.F., Dong, Y.H., Huang, L., Gong, Y.

Revision History  

• Version 1.0: 2020-06-24
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Structure summary