[English] 日本語
Yorodumi- PDB-8vom: Double alanine Apex domain mutant of bacteriophage P2 central spi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vom | ||||||
---|---|---|---|---|---|---|---|
Title | Double alanine Apex domain 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: 1.25 Å | ||||||
Authors | Leiman, P.G. / Miller, J.M. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8vom.cif.gz | 456.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8vom.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8vom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vom_validation.pdf.gz | 805.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8vom_full_validation.pdf.gz | 814.5 KB | Display | |
Data in XML | 8vom_validation.xml.gz | 34 KB | Display | |
Data in CIF | 8vom_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/8vom ftp://data.pdbj.org/pub/pdb/validation_reports/vo/8vom | HTTPS FTP |
-Related structure data
Related structure data | 8volC 8vonC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11876.268 Da / Num. of mol.: 6 / Mutation: H197A, H199A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteriophage P2 (virus) / Strain: Vir1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31340 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.76 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 5, 2021 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→50 Å / Num. obs: 306387 / % possible obs: 99.7 % / Redundancy: 7.42 % / Biso Wilson estimate: 12.55 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.064 / Net I/σ(I): 18.03 |
Reflection shell | Resolution: 1.25→1.28 Å / Redundancy: 7.16 % / Mean I/σ(I) obs: 5.24 / Num. unique obs: 22084 / CC1/2: 0.959 / Rrim(I) all: 0.483 / % possible all: 97.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→44.06 Å / SU ML: 0.0799 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 12.6145 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→44.06 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|