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Yorodumi- PDB-8c27: Domain 3 of Group B Streptococcus pilus protein as scaffold for t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c27 | ||||||
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Title | Domain 3 of Group B Streptococcus pilus protein as scaffold for the display of foreign epitopes | ||||||
Components | PI-2a backbone protein | ||||||
Keywords | MEMBRANE PROTEIN / Pilus protein / scaffold / epitopes. | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus agalactiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å | ||||||
Authors | Veggi, D. / Cappelli, L. / Cozzi, R. | ||||||
Funding support | 1items
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Citation | Journal: Faseb J. / Year: 2024 Title: Computational structure-based approach to study chimeric antigens using a new protein scaffold displaying foreign epitopes. Authors: Cappelli, L. / Cinelli, P. / Perrotta, A. / Veggi, D. / Audagnotto, M. / Tuscano, G. / Pansegrau, W. / Bartolini, E. / Rinaudo, D. / Cozzi, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c27.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c27.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 8c27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c27_validation.pdf.gz | 939.9 KB | Display | wwPDB validaton report |
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Full document | 8c27_full_validation.pdf.gz | 943 KB | Display | |
Data in XML | 8c27_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 8c27_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/8c27 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/8c27 | HTTPS FTP |
-Related structure data
Related structure data | 2xtlS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14666.284 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: B9UR22 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.41 Å3/Da / Density % sol: 63.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES with 20% w/v jeff ED-2001 pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96546 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96546 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→94.9 Å / Num. obs: 12062 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 60.74 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.63→94.9 Å / Num. unique obs: 12062 / CC1/2: 0.998 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XTL Resolution: 2.63→58.15 Å / SU ML: 0.4785 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.1437 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.1 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.63→58.15 Å
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Refine LS restraints |
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LS refinement shell |
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