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Yorodumi- PDB-4qnl: Crystal structure of tail fiber protein gp63.1 from E. coli phage G7C -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qnl | ||||||
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Title | Crystal structure of tail fiber protein gp63.1 from E. coli phage G7C | ||||||
Components | Tail fiber protein | ||||||
Keywords | HYDROLASE / tail fiber / G7C phage / hydrolase-type esterase / SGNH hydrolase-type esterase domain (IPR013831) / Adsorption of the phage on bacterial host / bacterial LPS digestion / tail fiber protein gp66 / selenomethionine derivative / distal end of the baseplate | ||||||
Function / homology | Function and homology information Seminal Fluid Protein PDC-109 (Domain B) - #80 / NE0471 N-terminal domain-like - #50 / NE0471 N-terminal domain-like / Tail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / Seminal Fluid Protein PDC-109 (Domain B) / Ribbon / 2-Layer Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Escherichia phage vB_EcoP_G7C (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.411 Å | ||||||
Authors | Riccio, C. / Browning, C. / Prokhorov, N. / Letarov, A. / Leiman, P.G. | ||||||
Citation | Journal: Mol. Microbiol. / Year: 2017 Title: Function of bacteriophage G7C esterase tailspike in host cell adsorption. Authors: Prokhorov, N.S. / Riccio, C. / Zdorovenko, E.L. / Shneider, M.M. / Browning, C. / Knirel, Y.A. / Leiman, P.G. / Letarov, A.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qnl.cif.gz | 337.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qnl.ent.gz | 286.7 KB | Display | PDB format |
PDBx/mmJSON format | 4qnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qnl_validation.pdf.gz | 456.1 KB | Display | wwPDB validaton report |
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Full document | 4qnl_full_validation.pdf.gz | 458.7 KB | Display | |
Data in XML | 4qnl_validation.xml.gz | 32.8 KB | Display | |
Data in CIF | 4qnl_validation.cif.gz | 47.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/4qnl ftp://data.pdbj.org/pub/pdb/validation_reports/qn/4qnl | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 94838.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage vB_EcoP_G7C (virus) / Gene: 63.1, gp63.1 / Plasmid: pET-23a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: G0XNW5 |
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-Non-polymers , 6 types, 341 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
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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: 2.41 Å3/Da / Density % sol: 48.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 150 mM Ammonium Sulphate, 34% PEE 797, 100 mM Bis-Tris pH 5.5; 1.5 ul protein @ 14.3 mg/ml + 1.5 ul well solution, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97969 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2012 / Details: dynamically bendable mirror |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97969 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→92 Å / Num. all: 67757 / Num. obs: 67757 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 57.1 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.41→2.56 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2 / Num. unique all: 10495 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.411→64.959 Å / SU ML: 0.29 / Isotropic thermal model: Isotropic with TLS / Cross valid method: FREE R / σ(F): 1.21 / Phase error: 23.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.411→64.959 Å
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Refine LS restraints |
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LS refinement shell |
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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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