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Yorodumi- PDB-4xon: Tailspike protein double mutant D339N/E372Q of E. coli bacterioph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xon | |||||||||
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Title | Tailspike protein double mutant D339N/E372Q of E. coli bacteriophage HK620 | |||||||||
Components | Tail spike protein | |||||||||
Keywords | VIRAL PROTEIN / 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 Similarity search - Function | |||||||||
Biological species | Salmonella phage HK620 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | |||||||||
Authors | Gohlke, U. / Broeker, N.K. / Heinemann, U. / Seckler, R. / Barbirz, S. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: to be published Title: Enthalpic cost of water removal from a hydrophobic glucose binding cavity on HK620 tailspike protein. Authors: Gohlke, U. / Broeker, N.K. / Kunstmann, S. / Santer, M. / Heinemann, U. / Lipowski, R. / Seckler, R. / 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. / Mueller, 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 | 4xon.cif.gz | 244.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xon.ent.gz | 195.3 KB | Display | PDB format |
PDBx/mmJSON format | 4xon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/4xon ftp://data.pdbj.org/pub/pdb/validation_reports/xo/4xon | HTTPS FTP |
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-Related structure data
Related structure data | 4xkvC 4xkwC 4xl9C 4xlaC 4xlcC 4xleC 4xlfC 4xlhC 4xm3C 4xmyC 4xn0C 4xn3C 4xnfC 4xopC 4xorSC 4xotC 4xqfC 4xr6C 4yejC 4yelC 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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Details | The biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -y+1,x-y,z and -x+y+1,-x+1,z. |
-Components
#1: Protein | Mass: 64588.293 Da / Num. of mol.: 1 / Fragment: head binding, UNP residues 112-710 / Mutation: D339N, E372Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella phage HK620 (virus) / Plasmid: pET11d / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9AYY6 | ||||
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#2: Chemical | ChemComp-TRS / | ||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: 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: 2.15 Å3/Da / Density % sol: 42.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 3.5 M Sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å | ||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 8, 2012 / Details: mirrors | ||||||||||||||||||||||||
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.1→43.65 Å / Num. obs: 33244 / % possible obs: 99.7 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.047 / Net I/σ(I): 14.5 / Num. measured all: 190913 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 5 % / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XOR Resolution: 2.1→43.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.1957 / WRfactor Rwork: 0.1362 / FOM work R set: 0.8148 / SU B: 12.731 / SU ML: 0.161 / SU R Cruickshank DPI: 0.2339 / SU Rfree: 0.1971 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.9 Å2 / Biso mean: 29.597 Å2 / Biso min: 12.29 Å2
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Refinement step | Cycle: final / Resolution: 2.1→43.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 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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