+Open data
-Basic information
Entry | Database: PDB / ID: 5tip | |||||||||||||||
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Title | The Structure of the Major Capsid protein of PBCV-1 | |||||||||||||||
Components | Major capsid protein | |||||||||||||||
Keywords | VIRAL PROTEIN | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Paramecium bursaria Chlorella virus 1 | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | |||||||||||||||
Authors | Klose, T. / De Castro, C. / Speciale, I. / Molinaro, A. / Van Etten, J.L. / Rossmann, M.G. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Structure of the chlorovirus PBCV-1 major capsid glycoprotein determined by combining crystallographic and carbohydrate molecular modeling approaches. Authors: De Castro, C. / Klose, T. / Speciale, I. / Lanzetta, R. / Molinaro, A. / Van Etten, J.L. / Rossmann, M.G. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tip.cif.gz | 714.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tip.ent.gz | 602.2 KB | Display | PDB format |
PDBx/mmJSON format | 5tip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tip_validation.pdf.gz | 5.8 MB | Display | wwPDB validaton report |
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Full document | 5tip_full_validation.pdf.gz | 5.8 MB | Display | |
Data in XML | 5tip_validation.xml.gz | 72.7 KB | Display | |
Data in CIF | 5tip_validation.cif.gz | 104.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/5tip ftp://data.pdbj.org/pub/pdb/validation_reports/ti/5tip | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 48068.430 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: P30328 |
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-Sugars , 6 types, 16 molecules
#2: Polysaccharide | 6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose-(1-2)-beta-L-rhamnopyranose-(1-4)-beta-D-xylopyranose- ...6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose-(1-2)-beta-L-rhamnopyranose-(1-4)-beta-D-xylopyranose-(1-4)-[alpha-D-mannopyranose-(1-3)-alpha-D-rhamnopyranose-(1-3)][alpha-D-galactopyranose-(1-2)]alpha-L-fucopyranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-rhamnopyranose-(1-3)-[alpha-D-galactopyranose-(1-2)][beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-rhamnopyranose-(1-3)-[alpha-D-galactopyranose-(1-2)][beta-D-xylopyranose-(1-4)]alpha-L-fucopyranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-L-rhamnopyranose-(1-4)-beta-D-xylopyranose-(1-4)-[alpha-D-galactopyranose-(1-2)][alpha-D- ...beta-L-rhamnopyranose-(1-4)-beta-D-xylopyranose-(1-4)-[alpha-D-galactopyranose-(1-2)][alpha-D-rhamnopyranose-(1-3)]alpha-L-fucopyranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-rhamnopyranose-(1-3)-[beta-L-rhamnopyranose-(1-4)-beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-rhamnopyranose-(1-3)-[beta-L-rhamnopyranose-(1-4)-beta-D-xylopyranose-(1-4)][alpha-D-galactopyranose-(1-2)]alpha-L-fucopyranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-BGC / | |
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-Non-polymers , 2 types, 1163 molecules
#7: Chemical | ChemComp-HG / #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3.4~4.0 M sodium formate, 50 mM Tris, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 13, 2002 | |||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2→100 Å / Num. obs: 148902 / % possible obs: 99 % / Redundancy: 40 % / Rmerge(I) obs: 0.132 | |||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.532 / % possible all: 98.8 |
-Processing
Software | Name: PHENIX / Version: (1.11.1_2575: ???) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→84.43 Å / Cross valid method: THROUGHOUT / σ(F): 5.6 / Phase error: 25.34 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→84.43 Å
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Refine LS restraints |
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LS refinement shell |
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