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- PDB-5e7t: Structure of the tripod (BppUct-A-L) from the baseplate of bacter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5e7t | ||||||
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Title | Structure of the tripod (BppUct-A-L) from the baseplate of bacteriophage Tuc2009 | ||||||
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![]() | VIRAL PROTEIN / bacteriophages / Lactococcus lactis / Siphoviridae / nanobody / receptor binding protein | ||||||
Function / homology | ![]() Baseplate upper protein, immunoglobulin like domain / Baseplate upper protein immunoglobulin like domain / BppU, N-terminal / BppU N-terminal domain / Lower baseplate protein, N-terminal / Lower baseplate protein N-terminal domain / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Legrand, P. / Collins, B. / Blangy, S. / Murphy, J. / Spinelli, S. / Gutierrez, C. / Richet, N. / Kellenberger, C. / Desmyter, A. / Mahony, J. ...Legrand, P. / Collins, B. / Blangy, S. / Murphy, J. / Spinelli, S. / Gutierrez, C. / Richet, N. / Kellenberger, C. / Desmyter, A. / Mahony, J. / van Sinderen, D. / Cambillau, C. | ||||||
![]() | ![]() Title: The Atomic Structure of the Phage Tuc2009 Baseplate Tripod Suggests that Host Recognition Involves Two Different Carbohydrate Binding Modules. Authors: Legrand, P. / Collins, B. / Blangy, S. / Murphy, J. / Spinelli, S. / Gutierrez, C. / Richet, N. / Kellenberger, C. / Desmyter, A. / Mahony, J. / van Sinderen, D. / Cambillau, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 423.8 KB | Display | ![]() |
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PDB format | ![]() | 349.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.4 KB | Display | ![]() |
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Full document | ![]() | 504 KB | Display | |
Data in XML | ![]() | 37.4 KB | Display | |
Data in CIF | ![]() | 51.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5e7bC ![]() 5e7fSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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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Components
-Minor structural protein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 14132.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 31884.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Major structural protein ... , 2 types, 4 molecules GHIL
#3: Protein | Mass: 18848.014 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#4: Protein | Mass: 18979.213 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 3 types, 67 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: by mixing 300 nl of protein (Na2HPO4, 10 mM; KH2PO4, 1.8 mM [pH7.4]; NaCl, 137 mM; KCl, 2.7 mM) with 100 nl precipitant solution (2 M Ammonium Sulfate, 0.1 M Na Hepes [pH 7]). PH range: 7.0 - 7.4 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→34.9 Å / Num. obs: 70164 / % possible obs: 99.8 % / Redundancy: 13.7 % / Biso Wilson estimate: 103.95 Å2 / Rmerge(I) obs: 0.187 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.9 / Mean I/σ(I) obs: 1.25 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5E7F RBP domain Resolution: 2.9→34.85 Å / Cor.coef. Fo:Fc: 0.9343 / Cor.coef. Fo:Fc free: 0.9233 / SU R Cruickshank DPI: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.278 / SU Rfree Blow DPI: 0.227 / SU Rfree Cruickshank DPI: 0.235
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Displacement parameters | Biso mean: 104.51 Å2
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Refine analyze | Luzzati coordinate error obs: 0.423 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→34.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.98 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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