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- PDB-9f4a: Interface between baseplate cup and extended tail tube/sheath of ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9f4a | |||||||||||||||||||||||||||
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Title | Interface between baseplate cup and extended tail tube/sheath of Klebsiella phage KP1 variant vB_Kpn_Lilla1 | |||||||||||||||||||||||||||
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![]() | VIRUS / Baseplate cup / baseplate wedge / fibers | |||||||||||||||||||||||||||
Function / homology | ![]() virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / viral release from host cell / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme ...virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / viral release from host cell / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / structural molecule activity / membrane Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.95 Å | |||||||||||||||||||||||||||
![]() | Orlova, E.V. / Isupov, M.N. | |||||||||||||||||||||||||||
Funding support | 1items
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![]() | ![]() Title: Baseplate cup of Klebsiella phage KP1 variant vB_Kpn_Lilla1 Authors: Orlova, E.V. / Isupov, M.N. | |||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 14.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 50186MC ![]() 9ev2C ![]() 9f4bC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 8 types, 120 molecules LeLfLgLhLiLjLSLTLULVLWLXLYLZLaLbLcLdBMBKBOBPBLBNBQBVBSBRBTBU...
#1: Protein | Mass: 138688.438 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 38263.664 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 33716.129 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein | Mass: 71695.094 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein | Mass: 18633.738 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein | Mass: 15382.360 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein | Mass: 43526.016 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein | Mass: 63317.457 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Baseplate wedge ... , 6 types, 72 molecules AXAWATASAVAUARAQANAMAPAOAYAZA0A1A2A3A4A9A6A5A8A7AdAcAfAeAbAa...
#4: Protein | Mass: 73689.242 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 119645.719 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | Mass: 38704.387 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 32380.195 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein | Mass: 66712.070 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) ![]() #13: Protein | Mass: 24693.420 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 1 types, 1 molecules 
#15: Chemical | ChemComp-CL / |
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-Details
Has ligand of interest | N |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: vB_Kpn_Lilla1 / Type: VIRUS / Entity ID: #3-#10, #12, #2, #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Natural host | Organism: Klebsiella |
Buffer solution | pH: 7.5 / Details: 100mM NaCl, 8mM MgSO4, 50mM Tris-HCl |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Klebsiella phage KP1 variant vB_Kpn_Lilla1 |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: EMS Lacey Carbon |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 92 % / Chamber temperature: 281 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS Details: Alignment procedure: EPU Autocoma and Autosrigmate Residual tilt (if alignment procedure is coma free, mrad): 68 Software used to collect images EPU 2.4, Tomo 5.13 Film/CCD/Direct electron ...Details: Alignment procedure: EPU Autocoma and Autosrigmate Residual tilt (if alignment procedure is coma free, mrad): 68 Software used to collect images EPU 2.4, Tomo 5.13 Film/CCD/Direct electron detector model*: post GIF K3 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 83505 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: OTHER |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 93.6 K / Temperature (min): 78.7 K / Residual tilt: 68 mradians |
Image recording | Average exposure time: 2 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 4 |
Image scans | Sampling size: 5 µm / Width: 4092 / Height: 5760 |
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Processing
EM software | Name: REFMAC / Version: 5.8.0258 / Category: model refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 34529 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2415 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.95→546.304 Å / Cor.coef. Fo:Fc: 0.862 / WRfactor Rwork: 0.45 / SU B: 91.285 / SU ML: 1.147 / Average fsc overall: 0.5353 / Average fsc work: 0.5353 / ESU R: 0.783 Details: Hydrogens have been added in their riding positions
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Solvent computation | Solvent model: BABINET MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 161.415 Å2
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Refine LS restraints |
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LS refinement shell | Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %
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