+Open data
-Basic information
Entry | Database: PDB / ID: 1k28 | ||||||
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Title | The Structure of the Bacteriophage T4 Cell-Puncturing Device | ||||||
Components |
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Keywords | HYDROLASE/STRUCTURAL PROTEIN / Triple-stranded beta-helix / OB fold / pseudohexamer / T4 tail lysozyme / HUB / gp27-gp5*-gp5C / HYDROLASE-STRUCTURAL PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information 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 / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...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 / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / symbiont entry into host cell / identical protein binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å | ||||||
Authors | Kanamaru, S. / Leiman, P.G. / Kostyuchenko, V.A. / Chipman, P.R. / Mesyanzhinov, V.V. / Arisaka, F. / Rossmann, M.G. | ||||||
Citation | Journal: Nature / Year: 2002 Title: Structure of the cell-puncturing device of bacteriophage T4. Authors: Kanamaru, S. / Leiman, P.G. / Kostyuchenko, V.A. / Chipman, P.R. / Mesyanzhinov, V.V. / Arisaka, F. / Rossmann, M.G. | ||||||
History |
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Remark 999 | SEQUENCE THE AUTHORS MAINTAIN THAT THEIR SEQUENCE IS CORRECT. | ||||||
Remark 600 | HETEROGEN THE AUTHORS BELIEVE THAT THE K AND PO4 IONS ARE PRESENT INSIDE THE PROTEIN FROM THE ...HETEROGEN THE AUTHORS BELIEVE THAT THE K AND PO4 IONS ARE PRESENT INSIDE THE PROTEIN FROM THE MOMENT IT FOLDS AND ARE PROBABLY A PART OF THE BIOLOGICAL ASSEMBLY. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k28.cif.gz | 199.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k28.ent.gz | 163.8 KB | Display | PDB format |
PDBx/mmJSON format | 1k28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k28_validation.pdf.gz | 460.2 KB | Display | wwPDB validaton report |
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Full document | 1k28_full_validation.pdf.gz | 508.8 KB | Display | |
Data in XML | 1k28_validation.xml.gz | 43.3 KB | Display | |
Data in CIF | 1k28_validation.cif.gz | 60.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/1k28 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/1k28 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a hexamer generated from the two polypeptides in the asymmetric unit by the operations: -y,x-y,z and -x+y,-x,z |
-Components
#1: Protein | Mass: 64313.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: 5 / Plasmid: pET-29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16009, lysozyme |
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#2: Protein | Mass: 45228.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: 27 / Plasmid: pET-29b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P17172 |
#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.18 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, Tris, Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9786, 0.9783, 1.0188, 0.9414 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 2, 2001 / Details: bent cylindrical Si-mirror (Rh coating) | |||||||||||||||
Radiation | Monochromator: Si(111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.9→50 Å / Num. all: 32046 / Num. obs: 31712 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 66.4 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 11.6 | |||||||||||||||
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 10.3 / Num. unique all: 1581 / Rsym value: 0.289 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.9→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 50 Å / σ(F): 0 / Rfactor obs: 0.21 / Rfactor Rfree: 0.28 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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