+Open data
-Basic information
Entry | Database: PDB / ID: 3riq | ||||||
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Title | Siphovirus 9NA tailspike receptor binding domain | ||||||
Components | Tailspike protein | ||||||
Keywords | VIRAL PROTEIN / right handed beta-helix / tailspike / endorhamnosidase / lipopolysaccharide | ||||||
Function / homology | Function and homology information biological process involved in interaction with host / viral life cycle / virion component Similarity search - Function | ||||||
Biological species | Siphovirus 9NA | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Andres, D. / Roske, Y. / Doering, C. / Heinemann, U. / Seckler, R. / Barbirz, S. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2012 Title: Tail morphology controls DNA release in two Salmonella phages with one lipopolysaccharide receptor recognition system. Authors: Andres, D. / Roske, Y. / Doering, 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 | 3riq.cif.gz | 250 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3riq.ent.gz | 200.5 KB | Display | PDB format |
PDBx/mmJSON format | 3riq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3riq_validation.pdf.gz | 429.4 KB | Display | wwPDB validaton report |
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Full document | 3riq_full_validation.pdf.gz | 431.7 KB | Display | |
Data in XML | 3riq_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 3riq_validation.cif.gz | 43.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/3riq ftp://data.pdbj.org/pub/pdb/validation_reports/ri/3riq | HTTPS FTP |
-Related structure data
Related structure data | 2vfmS S: Starting model for refinement |
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Similar 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: 59406.215 Da / Num. of mol.: 1 Fragment: C-terminal fragment, receptor binding domain, residues 131-673 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Siphovirus 9NA / Plasmid: pET 11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G8GV21*PLUS |
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#2: Chemical | ChemComp-GOL / |
#3: 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: 2.33 Å3/Da / Density % sol: 47.28 % |
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Crystal grow | Temperature: 293 K / pH: 6.5 Details: 20% PEG 5000 MME, 0.1M BisTris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 23, 2010 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→33.3 Å / Num. obs: 87485 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.071 / Rsym value: 0.065 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 2.59 / Rsym value: 0.686 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VFM Resolution: 1.5→33.35 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.332 / SU ML: 0.039 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.063 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.858 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→33.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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