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Yorodumi- PDB-3th0: P22 Tailspike complexed with S.Paratyphi O antigen octasaccharide -
+Open data
-Basic information
Entry | Database: PDB / ID: 3th0 | |||||||||
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Title | P22 Tailspike complexed with S.Paratyphi O antigen octasaccharide | |||||||||
Components | Bifunctional tail protein | |||||||||
Keywords | VIRAL PROTEIN / VIRAL ADHESION PROTEIN / RECEPTOR / ENDOGLYCOSIDASE / CARBOHYDRATE / CELL RECEPTOR / RECOGNITION / BINDING PROTEIN LIPOPOLYSACCHARIDE / beta helix / host recognition / Bacteriophage P22 baseplate / HYDROLASE | |||||||||
Function / homology | Function and homology information endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell Similarity search - Function | |||||||||
Biological species | Enterobacteria phage P22 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Andres, D. / Gohlke, U. / Heinemann, U. / Seckler, R. / Barbirz, S. | |||||||||
Citation | Journal: Glycobiology / Year: 2013 Title: An essential serotype recognition pocket on phage P22 tailspike protein forces Salmonella enterica serovar Paratyphi A O-antigen fragments to bind as nonsolution conformers. Authors: Andres, D. / Gohlke, U. / Broeker, N.K. / Schulze, S. / Rabsch, W. / Heinemann, U. / Barbirz, S. / Seckler, R. #1: Journal: Science / Year: 1994 Title: Crystal structure of P22 tailspike protein: interdigitated subunits in a thermostable trimer. Authors: Steinbacher, S. / Seckler, R. / Miller, S. / Steipe, B. / Huber, R. / Reinemer, P. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996 Title: Crystal structure of phage P22 tailspike protein complexed with Salmonella sp. O-antigen receptors. Authors: Steinbacher, S. / Baxa, U. / Miller, S. / Weintraub, A. / Seckler, R. / Huber, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3th0.cif.gz | 247.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3th0.ent.gz | 196.2 KB | Display | PDB format |
PDBx/mmJSON format | 3th0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/3th0 ftp://data.pdbj.org/pub/pdb/validation_reports/th/3th0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 60265.270 Da / Num. of mol.: 1 / Fragment: UNP residues 109-657 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage P22 (virus) / Gene: 9, phage p22 gene 9 / Plasmid: pTSF1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 References: UniProt: P12528, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds | ||
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#2: Polysaccharide | alpha-D-galactopyranose-(1-2)-[alpha-D-Paratopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-alpha-L- ...alpha-D-galactopyranose-(1-2)-[alpha-D-Paratopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-alpha-L-rhamnopyranose-(1-3)-alpha-D-galactopyranose-(1-2)-[alpha-D-Paratopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-alpha-L-rhamnopyranose | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal |
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Crystal grow |
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-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: Oct 12, 2010 Details: mirrors, double crystal monochromator, MD2 microdiffractometer, MK3-minikappa |
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: 1.75→33.27 Å / Num. obs: 58030 / % possible obs: 99.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 11.55 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 4247 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ENSEMBLE OF PDB ENTRIES 2VFM, 2VFN, and 2VFQ Resolution: 1.75→33.27 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.286 / SU ML: 0.032 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.308 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→33.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.749→1.795 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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