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Yorodumi- PDB-6nw9: CRYSTAL STRUCTURE OF A TAILSPIKE PROTEIN 3 (TSP3, ORF212) FROM ES... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nw9 | ||||||
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Title | CRYSTAL STRUCTURE OF A TAILSPIKE PROTEIN 3 (TSP3, ORF212) FROM ESCHERICHIA COLI O157:H7 BACTERIOPHAGE CBA120 | ||||||
Components | Tailspike protein | ||||||
Keywords | VIRAL PROTEIN / PARALLEL BETA HELIX / PUTATIVE ENDO-GLYCOSIDASE / BACTERIAL POLYSACCHARIDE / PHAGE TAIL / PHAGE CBA120 | ||||||
Function / homology | Function and homology information biological process involved in interaction with host / viral life cycle / virion component / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia virus CBA120 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | ||||||
Authors | Greenfield, J.Y. / Herzberg, O. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2019 Title: Structure and tailspike glycosidase machinery of ORF212 from E. coli O157:H7 phage CBA120 (TSP3). Authors: Greenfield, J. / Shang, X. / Luo, H. / Zhou, Y. / Heselpoth, R.D. / Nelson, D.C. / Herzberg, O. #1: Journal: PLoS ONE / Year: 2014 Title: Crystal structure of ORF210 from E. coli O157:H1 phage CBA120 (TSP1), a putative tailspike protein. Authors: Chen, C. / Bales, P. / Greenfield, J. / Heselpoth, R.D. / Nelson, D.C. / Herzberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nw9.cif.gz | 423.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nw9.ent.gz | 337.4 KB | Display | PDB format |
PDBx/mmJSON format | 6nw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nw9_validation.pdf.gz | 548.3 KB | Display | wwPDB validaton report |
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Full document | 6nw9_full_validation.pdf.gz | 567.4 KB | Display | |
Data in XML | 6nw9_validation.xml.gz | 85.7 KB | Display | |
Data in CIF | 6nw9_validation.cif.gz | 130.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/6nw9 ftp://data.pdbj.org/pub/pdb/validation_reports/nw/6nw9 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 68731.547 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia virus CBA120 / Gene: orf212 / Plasmid: PBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami / References: UniProt: G3M191 |
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-Non-polymers , 10 types, 1923 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-PEG / #9: Chemical | ChemComp-PGE / | #10: Chemical | #11: 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: 2.54 Å3/Da / Density % sol: 51.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 18% PEG 8000, 0.2M sodium chloride, 0.1M N-Cyclohexyl-2-aminoethanesulfonic acid (CHES) PH range: 9.0-9.8 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97932 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 18, 2015 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97932 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→54.158 Å / Num. obs: 175535 / % possible obs: 99.69 % / Redundancy: 2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 17301 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.85→54.158 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→54.158 Å
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Refine LS restraints |
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LS refinement shell |
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