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Yorodumi- PDB-4xla: Tailspike protein mutant D339A of E. coli bacteriophage HK620 IN ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xla | |||||||||
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Title | Tailspike protein mutant D339A of E. coli bacteriophage HK620 IN COMPLEX WITH PENTASACCHARIDE | |||||||||
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 | Enterobacteria phage HK620 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 | 4xla.cif.gz | 261.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xla.ent.gz | 206.9 KB | Display | PDB format |
PDBx/mmJSON format | 4xla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/4xla ftp://data.pdbj.org/pub/pdb/validation_reports/xl/4xla | HTTPS FTP |
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-Related structure data
Related structure data | 4xkvC 4xkwC 4xl9C 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 (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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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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 64661.348 Da / Num. of mol.: 1 / Fragment: head binding, unp residues 111-710 / Mutation: D339A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage HK620 (virus) / Plasmid: pET11d / Production host: Escherichia coli BL21 (bacteria) / 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, 836 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: 2.15 Å3/Da / Density % sol: 42.71 % |
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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 Sodiumformate |
-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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 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: 1.47→43.66 Å / Num. obs: 95097 / % possible obs: 99.5 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.036 / Net I/σ(I): 11.9 / Num. measured all: 369496 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4xm3 Resolution: 1.47→43.66 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.1545 / WRfactor Rwork: 0.127 / FOM work R set: 0.87 / SU B: 2.648 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0606 / SU Rfree: 0.0625 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.063 / 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: 76.1 Å2 / Biso mean: 16.398 Å2 / Biso min: 8.71 Å2
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Refinement step | Cycle: final / Resolution: 1.47→43.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.47→1.508 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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