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Open data
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Basic information
Entry | Database: PDB / ID: 4xl9 | |||||||||
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Title | Tailspike protein mutant D339A of E. coli bacteriophage HK620 | |||||||||
![]() | Tail spike protein | |||||||||
![]() | VIRAL PROTEIN / beta helix / protein-carbohydrate complex / pectin lyase fold | |||||||||
Function / homology | ![]() biological process involved in interaction with host / viral life cycle / virion component / metal ion binding 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 | ![]() | 243.2 KB | Display | ![]() |
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PDB format | ![]() | 193.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.7 KB | Display | ![]() |
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Full document | ![]() | 452.9 KB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 39.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xkvC ![]() 4xkwC ![]() 4xlaC ![]() 4xlcC ![]() 4xleC ![]() 4xlfC ![]() 4xlhC ![]() 4xm3SC ![]() 4xmyC ![]() 4xn0C ![]() 4xn3C ![]() 4xnfC ![]() 4xonC ![]() 4xopC ![]() 4xorC ![]() 4xotC ![]() 4xqfC ![]() 4xr6C ![]() 4yejC ![]() 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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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. |
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Components
#1: Protein | Mass: 64334.059 Da / Num. of mol.: 1 / Fragment: UNP residues 114-710 / Mutation: D339A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-TRS / |
#3: Chemical | ChemComp-FMT / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.83 % |
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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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2014 / 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: 2.02→42.93 Å / Num. obs: 35142 / % possible obs: 95.8 % / Redundancy: 3.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.056 / Net I/σ(I): 8 / Num. measured all: 136596 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XM3 Resolution: 2.02→42.93 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2322 / WRfactor Rwork: 0.1722 / FOM work R set: 0.7755 / SU B: 12.36 / SU ML: 0.166 / SU R Cruickshank DPI: 0.2394 / SU Rfree: 0.1966 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / 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: 69.02 Å2 / Biso mean: 26.399 Å2 / Biso min: 11.47 Å2
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Refinement step | Cycle: final / Resolution: 2.02→42.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.072 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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