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- PDB-9eul: Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 c... -

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Basic information

Entry
Database: PDB / ID: 9eul
TitleCryo-EM structure of Staphylococcus aureus bacteriophage phi812 central spike protein - knob and petal domains
ComponentsGP-PDE domain-containing protein
KeywordsVIRAL PROTEIN / bacteriophage / phage / contractile / phi812 / spike / central spike / TIM
Function / homologyGlycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / GP-PDE domain-containing protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsBinovsky, J. / Pichel-Beleiro, A. / van Raaij, M.J. / Plevka, P.
Funding supportEuropean Union, Czech Republic, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Other governmentLX22NP05103 Czech Republic
CitationJournal: To Be Published
Title: Cell attachment and tail contraction of S. aureus phage phi812
Authors: Binovsky, J. / Pichel-Beleiro, A. / van Raaij, M.J. / Plevka, P.
History
DepositionMar 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GP-PDE domain-containing protein


Theoretical massNumber of molelcules
Total (without water)94,2741
Polymers94,2741
Non-polymers00
Water00
1
A: GP-PDE domain-containing protein

A: GP-PDE domain-containing protein

A: GP-PDE domain-containing protein


Theoretical massNumber of molelcules
Total (without water)282,8233
Polymers282,8233
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
MethodUCSF CHIMERA

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Components

#1: Protein GP-PDE domain-containing protein / central spike protein - knob and petal domains


Mass: 94274.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage 812 (virus) / Gene: 812_115, 812a_115, 812F1_115, K1/420_115, K1_115 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U1WFD7
Has protein modificationN

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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: Central spike protein - knob and petal domains / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Staphylococcus phage 812 (virus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7 / Details: sample diluted 10x with water before vitrification
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMSodium Potassium PhosphateKNaO4P-1
2200 mMSodium ChlorideNaCl1
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: sample diluted 10x with water before vitrification
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 8 sec. / Electron dose: 57 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3120
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2SerialEMimage acquisition
4GctfCTF correction
7UCSF Chimera1.15model fitting
9RELION3.1initial Euler assignment
10RELION5.0betafinal Euler assignment
11RELION5.0betaclassification
12RELION5.0beta3D reconstruction
13PHENIX1.21model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 487160
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135736 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: Chimera; Isolde
Atomic model building
ID 3D fitting-IDDetailsSource nameType
11Xray structureOtherexperimental model
21manual buildingOtherin silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0019330
ELECTRON MICROSCOPYf_angle_d0.37212639
ELECTRON MICROSCOPYf_dihedral_angle_d8.2463441
ELECTRON MICROSCOPYf_chiral_restr0.041401
ELECTRON MICROSCOPYf_plane_restr0.0031626

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