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Yorodumi- PDB-2fkk: Crystal structure of the C-terminal domain of the bacteriophage T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fkk | ||||||
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Title | Crystal structure of the C-terminal domain of the bacteriophage T4 gene product 10 | ||||||
Components | Baseplate structural protein Gp10 | ||||||
Keywords | VIRAL PROTEIN / Bacteriophage T4 / Baseplate / Tail / Evolution / gp10 / Structural comparisons | ||||||
Function / homology | Function and homology information virus tail, baseplate / viral tail assembly / viral release from host cell Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.2 Å | ||||||
Authors | Leiman, P.G. / Shneider, M.M. / Mesyanzhinov, V.V. / Rossmann, M.G. | ||||||
Citation | Journal: J Mol Biol / Year: 2006 Title: Evolution of bacteriophage tails: Structure of T4 gene product 10. Authors: Petr G Leiman / Mikhail M Shneider / Vadim V Mesyanzhinov / Michael G Rossmann / Abstract: The success of tailed bacteriophages to infect cells far exceeds that of most other viruses on account of their specialized tail and associated baseplate structures. The baseplate protein gene ...The success of tailed bacteriophages to infect cells far exceeds that of most other viruses on account of their specialized tail and associated baseplate structures. The baseplate protein gene product (gp) 10 of bacteriophage T4, whose structure was determined to 1.2 A resolution, was fitted into the cryo-electron microscopy structures of the pre and post-infection conformations of the virus. gp10 functions as a molecular lever that rotates and extends the hinged short tail fibers to facilitate cell attachment. The central folding motif of the gp10 trimer is similar to that of the baseplate protein gp11 and to the receptor-binding domain of the short tail fiber, gp12. The three proteins comprise the periphery of the baseplate and interact with each other. The structural and functional similarities of gp10, gp11, and gp12 and their sequential order in the T4 genome suggest that they evolved separately, subsequent to gene triplication from a common ancestor. Such events are usual in the evolution of complex organelles from a common primordial molecule. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fkk.cif.gz | 135.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fkk.ent.gz | 108.5 KB | Display | PDB format |
PDBx/mmJSON format | 2fkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/2fkk ftp://data.pdbj.org/pub/pdb/validation_reports/fk/2fkk | HTTPS FTP |
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-Related structure data
-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 trimer. The second and third chains can be generated by using the symmetry operators of the crystallographic threefold axis: -y+1, x-y, z and y-x+1, -x+1, z |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22432.246 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Mutation: A442E, A530T 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 / Strain: D / Gene: 10 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P10928 |
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-Non-polymers , 5 types, 370 molecules
#2: Chemical | ChemComp-BR / | ||
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#3: Chemical | ChemComp-PO3 / | ||
#4: Chemical | ChemComp-TRS / | ||
#5: Chemical | ChemComp-EDO / #6: 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: 3.75 Å3/Da / Density % sol: 67.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 2.3 Details: 6% PEG1000, 8% PEG8000, 100 mM glycine-HCl pH 2.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2005 Details: Bent conical Si-mirror (Rh coated), Bent Ge(111) monochromator |
Radiation | Monochromator: Bent conical Si-mirror (Rh coated), Bent Ge(111) monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30 Å / Num. all: 106155 / Num. obs: 105624 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5221 / Rsym value: 0.39 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING Starting model: none Resolution: 1.2→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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