9IMJ

Bacteriophage T6 topoisomerase II ATPase domain crystal strcuture

• PDB DOI: https://doi.org/10.2210/pdb9IMJ/pdb

• Classification: ISOMERASE
• Organism(s): Enterobacteria phage T6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-03 Released: 2024-09-25 
• Deposition Author(s): Xin, Y.H., Chen, Y.T.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.289 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 

Starting Model: in silico

Literature

Bacteriophage T6 topoisomerase II ATPase domain crystal strcuture

Xin, Y.H., Chen, Y.T.

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: electron microscopy

Macromolecule Content

• Total Structure Weight: 44.22 kDa 
• Atom Count: 3,020 
• Modelled Residue Count: 375 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase (ATP-hydrolyzing)	A	386	Enterobacteria phage T6	Mutation(s): 0  Gene Names: EcT6_00003 EC: 5.6.2.2
UniProt
Find proteins for A0A346FJ89 (Enterobacteria phage T6) Explore A0A346FJ89  Go to UniProtKB:  A0A346FJ89

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.289 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.989	α = 90
b = 90.989	β = 90
c = 102.9	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Xin, Y.H., Chen, Y.T.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release