[English] 日本語
Yorodumi- PDB-4yel: Tailspike protein double mutant D339A/E372A of E. coli bacterioph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yel | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Tailspike protein double mutant D339A/E372A of E. coli bacteriophage HK620 in complex with hexasaccharide | ||||||||||||
Components | Tail spike protein | ||||||||||||
Keywords | METAL BINDING 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: 1.72 Å | ||||||||||||
Authors | Gohlke, U. / Broeker, N.K. / Heinemann, U. / Seckler, R. / Barbirz, S. | ||||||||||||
Funding support | Germany, 1items
| ||||||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4yel.cif.gz | 262.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4yel.ent.gz | 206.8 KB | Display | PDB format |
PDBx/mmJSON format | 4yel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/4yel ftp://data.pdbj.org/pub/pdb/validation_reports/ye/4yel | HTTPS FTP |
---|
-Related structure data
Related structure data | 4xkvC 4xkwC 4xl9C 4xlaC 4xlcC 4xleC 4xlfC 4xlhC 4xm3C 4xmyC 4xn0C 4xn3C 4xnfC 4xonC 4xopC 4xorC 4xotC 4xqfC 4xr6C 4yejC 4avzS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 64147.895 Da / Num. of mol.: 1 / Fragment: head binding, RESIDUES 115-710 / Mutation: D339A, E372A 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 |
---|---|
#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)-[alpha-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 772 molecules
#3: Chemical | ChemComp-TRS / | ||||
---|---|---|---|---|---|
#4: Chemical | ChemComp-FMT / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.4 % |
---|---|
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 | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 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: 0.91841 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.72→43.67 Å / Num. obs: 60326 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.041 / Net I/σ(I): 17.9 / Num. measured all: 364165 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AVZ Resolution: 1.72→43.67 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1432 / WRfactor Rwork: 0.1121 / FOM work R set: 0.8872 / SU B: 4.195 / SU ML: 0.069 / SU R Cruickshank DPI: 0.0937 / SU Rfree: 0.0931 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 64.49 Å2 / Biso mean: 16.164 Å2 / Biso min: 7.82 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.72→43.67 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.72→1.765 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|