7L6S

Crystal structure of the ATPase and transducer domains of DNA topoisomerase II from Balamuthia mandrillaris CDC:V039: baboon/San Diego/1986

• PDB DOI: https://doi.org/10.2210/pdb7L6S/pdb

• Classification: ISOMERASE
• Organism(s): Balamuthia mandrillaris
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-12-23 Released: 2021-01-13 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.196 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

Crystal Structure of the ATPase and transducer domains of DNA topoisomerase II from Balamuthia mandrillaris Lepto ID: CDC:V039: baboon/San Diego/1986

Abendroth, J., Fox III, D., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 49 kDa 
• Atom Count: 3,495 
• Modelled Residue Count: 396 
• Deposited Residue Count: 423 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase II	A	423	Balamuthia mandrillaris	Mutation(s): 0  EC: 5.6.2.2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.196 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.18430/m37l6s

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.77	α = 90
b = 187.25	β = 90
c = 61.69	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2021-01-20
  Changes: Structure summary
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description