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Open data
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Basic information
Entry | Database: PDB / ID: 9nwm | |||||||||||||||||||||||||||
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Title | Pseudomonas phage Pa223 Portal (C12 symmetry) | |||||||||||||||||||||||||||
![]() | Portal (Connector) protein | |||||||||||||||||||||||||||
![]() | VIRUS / Constituent protein / Structural protein / Phage tail component | |||||||||||||||||||||||||||
Function / homology | : / Phage SU10 portal protein / Portal (Connector) protein![]() | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||||||||||||||||||||
![]() | Hou, C.F.D. / Cingolani, G. / Lokareddy, K.R. | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: High-resolution cryo-EM analysis of the therapeutic Pseudomonas phage Pa223 Authors: Hou, C.F.D. / Lokareddy, K.R. / Cingolani, G. | |||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 203.6 KB | Display | |
Data in CIF | ![]() | 306.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 49887MC ![]() 9nwiC ![]() 9nxkC ![]() 9nxoC ![]() 9nxpC ![]() 9ny2C ![]() 9ny6C 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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Components
#1: Protein | Mass: 81180.578 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() Has protein modification | Y | |
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-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: Pseudomonas virus Pa223 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Pseudomonas aeruginosa |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 62000 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46120 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.01 Å2 | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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