6K8O | pdb_00006k8o

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.259 (Depositor), 0.261 (DCC)
R-Value Work:
0.220 (Depositor), 0.214 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6K8O

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97ZJ8
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (5'-D(GPCPAPAPGPGPTPC)-3')	B	8	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.259 (Depositor), 0.261 (DCC)
R-Value Work: 0.220 (Depositor), 0.214 (DCC)
R-Value Observed: 0.222 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2020-06-24

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.