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Yorodumi- PDB-8vol: Apex domain deletion mutant of bacteriophage P2 central spike pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vol | ||||||
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Title | Apex domain deletion mutant of bacteriophage P2 central spike protein, membrane-piercing module | ||||||
Components | Spike protein | ||||||
Keywords | VIRAL PROTEIN / Membrane-piercing / phage / baseplate / trimer | ||||||
Function / homology | Function and homology information virus tail, baseplate / viral tail assembly / symbiont genome entry into host cell via pore formation in plasma membrane / entry receptor-mediated virion attachment to host cell / metal ion binding Similarity search - Function | ||||||
Biological species | Bacteriophage P2 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å | ||||||
Authors | Leiman, P.G. / Miller, J.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: bioRxiv / Year: 2023 Title: Function of the bacteriophage P2 baseplate central spike Apex domain in the infection process. Authors: Miller, J.M. / Knyazhanskaya, E.S. / Buth, S.A. / Prokhorov, N.S. / Leiman, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vol.cif.gz | 489 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vol.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8vol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vol_validation.pdf.gz | 689.6 KB | Display | wwPDB validaton report |
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Full document | 8vol_full_validation.pdf.gz | 694.8 KB | Display | |
Data in XML | 8vol_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 8vol_validation.cif.gz | 58.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/8vol ftp://data.pdbj.org/pub/pdb/validation_reports/vo/8vol | HTTPS FTP |
-Related structure data
Related structure data | 8vomC 8vonC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10691.044 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: Exogenous C-terminal leucine was added by mutagenesis. Source: (gene. exp.) Bacteriophage P2 (virus) / Strain: Vir1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31340 #2: Chemical | ChemComp-PTY / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 26-33% Pentaerythritol ethoxylate (15/4 EO/OH) aka PEE-797, 100 mM Bis-Tris or MES pH 6.0-6.5 PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.7749 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 15, 2020 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 0.9→26.73 Å / Num. obs: 821847 / % possible obs: 94.5 % / Redundancy: 3.33 % / Biso Wilson estimate: 7.29 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.083 / Net I/σ(I): 9.69 |
Reflection shell | Resolution: 0.9→0.93 Å / Redundancy: 3.15 % / Mean I/σ(I) obs: 2.07 / Num. unique obs: 55324 / CC1/2: 0.861 / Rrim(I) all: 0.544 / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.9→26.73 Å / SU ML: 0.0611 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 11.8634 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.9→26.73 Å
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Refine LS restraints |
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LS refinement shell |
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