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- PDB-4yej: Tailspike protein double mutant D339A/E372Q of E. coli bacterioph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yej | ||||||||||||
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Title | Tailspike protein double mutant D339A/E372Q of E. coli bacteriophage HK620 in complex with pentasaccharide | ||||||||||||
![]() | Tail spike protein | ||||||||||||
![]() | METAL BINDING PROTEIN / ![]() | ||||||||||||
Function / homology | ![]() biological process involved in interaction with host / ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Gohlke, U. / Broeker, N.K. / Heinemann, U. / Seckler, R. / Barbirz, S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266 KB | Display | ![]() |
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PDB format | ![]() | 209.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4xkvC ![]() 4xkwC ![]() 4xl9C ![]() 4xlaC ![]() 4xlcC ![]() 4xleC ![]() 4xlfC ![]() 4xlhC ![]() 4xm3SC ![]() 4xmyC ![]() 4xn0C ![]() 4xn3C ![]() 4xnfC ![]() 4xonC ![]() 4xopC ![]() 4xorC ![]() 4xotC ![]() 4xqfC ![]() 4xr6C ![]() 4yelC 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 64333.074 Da / Num. of mol.: 1 / Fragment: head binding, UNP residues 114-710 / Mutation: D339A, E372Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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-alpha-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 875 molecules ![](data/chem/img/TRS.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-TRS / ![]() | ||||
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#4: Chemical | ![]() #5: Chemical | #6: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.22 % |
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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 Sodiumformiate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
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![]() | |||||||||||||||||||||||||||
Reflection | Resolution: 1.4→43.68 Å / Num. obs: 108242 / % possible obs: 98 % / Redundancy: 5.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.028 / Net I/σ(I): 16.7 / Num. measured all: 562783 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4XM3 Resolution: 1.4→43.68 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1576 / WRfactor Rwork: 0.1293 / FOM work R set: 0.8859 / SU B: 2.175 / SU ML: 0.043 / SU R Cruickshank DPI: 0.0549 / SU Rfree: 0.0578 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.058 / 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: 66.95 Å2 / Biso mean: 13.794 Å2 / Biso min: 6.14 Å2
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Refinement step | Cycle: final / Resolution: 1.4→43.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.402→1.438 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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