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- PDB-8yo1: structure of phage T6 topoisomerase II ATPase domain bound with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 8yo1
Titlestructure of phage T6 topoisomerase II ATPase domain bound with AMPPNP
ComponentsDNA topoisomerase (ATP-hydrolyzing)
KeywordsISOMERASE / topoisomerase II
Function / homology
Function and homology information


sister chromatid segregation / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA binding / ATP binding
Similarity search - Function
: / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / DNA topoisomerase, type IIA-like domain superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...: / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / DNA topoisomerase, type IIA-like domain superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA topoisomerase (ATP-hydrolyzing)
Similarity search - Component
Biological speciesEnterobacteria phage T6 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsChen, Y.T. / Xin, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To be published
Title: structure of phage T6 topoisomerase II ATPase domain bound with AMPPNP
Authors: Chen, Y.T. / Xin, Y.H. / Xian, R.Q.
History
DepositionMar 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: DNA topoisomerase (ATP-hydrolyzing)
D: DNA topoisomerase (ATP-hydrolyzing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,5115
Polymers138,4752
Non-polymers1,0373
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein DNA topoisomerase (ATP-hydrolyzing) / phage T6 topoisomerase II gp39 subunit


Mass: 69237.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T6 (virus) / Gene: EcT6_00003 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A346FJ89, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Phage T6 topoisomerase II ATPase domain bound with AMPPNP
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Enterobacteria phage T6 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80615 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036076
ELECTRON MICROSCOPYf_angle_d0.5568200
ELECTRON MICROSCOPYf_dihedral_angle_d8.717816
ELECTRON MICROSCOPYf_chiral_restr0.047910
ELECTRON MICROSCOPYf_plane_restr0.0041056

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