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Yorodumi- PDB-6g0x: TAILSPIKE PROTEIN OF E. COLI BACTERIOPHAGE HK620 IN COMPLEX WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g0x | |||||||||
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Title | TAILSPIKE PROTEIN OF E. COLI BACTERIOPHAGE HK620 IN COMPLEX WITH PENTASACCHARIDE | |||||||||
Components | Tail spike protein | |||||||||
Keywords | HYDROLASE / BETA HELIX / PROTEIN-CARBOHYDRATE COMPLEX / PECTIN LYASE FOLD | |||||||||
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 | Salmonella phage HK620 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å | |||||||||
Authors | Gohlke, U. / Broeker, N.K. / Seckler, R. / Barbirz, S. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: Solvent Networks Tune Thermodynamics of Oligosaccharide Complex Formation in an Extended Protein Binding Site. Authors: Kunstmann, S. / Gohlke, U. / Broeker, N.K. / Roske, Y. / Heinemann, U. / Santer, M. / Barbirz, S. #1: Journal: Glycobiology / Year: 2013 Title: Single amino acid exchange in bacteriophage HK620 tailspike protein results in thousand-fold increase of its oligosaccharide affinity. Authors: Broeker, N.K. / Gohlke, U. / Muller, J.J. / Uetrecht, C. / Heinemann, U. / Seckler, R. / Barbirz, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g0x.cif.gz | 262.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g0x.ent.gz | 209.8 KB | Display | PDB format |
PDBx/mmJSON format | 6g0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/6g0x ftp://data.pdbj.org/pub/pdb/validation_reports/g0/6g0x | HTTPS FTP |
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-Related structure data
Related structure data | 6gvpC 6gvrC 2vjiS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 64590.270 Da / Num. of mol.: 1 / Fragment: HEAD BINDING, RESIDUES 112-710 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella phage HK620 (virus) / Plasmid: PET11D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9AYY6 |
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#2: Polysaccharide | alpha-L-rhamnopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose- ...alpha-L-rhamnopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)]alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 813 molecules
#3: Chemical | ChemComp-TRS / | ||||
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#4: Chemical | ChemComp-FMT / #5: Chemical | #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: 2.16 Å3/Da / Density % sol: 43.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M TRIS-HCL, 3.5 M SODIUMFORMIATE / PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 6, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→43.21 Å / Num. obs: 107055 / % possible obs: 98.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.41→1.43 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 2 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2vji Resolution: 1.41→43.21 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.407 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.06 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.41→43.21 Å
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Refine LS restraints |
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