+Open data
-Basic information
Entry | Database: PDB / ID: 7o5y | ||||||
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Title | PilA minor pilin of Streptococcus sanguinis type IV pili | ||||||
Components | Type IV pilus biogenesis protein PilA | ||||||
Keywords | STRUCTURAL PROTEIN / pilin | ||||||
Function / homology | membrane => GO:0016020 / Type IV pilus biogenesis protein PilA Function and homology information | ||||||
Biological species | Streptococcus sanguinis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å | ||||||
Authors | Sheppard, D. / Pelicic, V. / Berry, J.B. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Characterization of a glycan-binding complex of minor pilins completes the analysis of Streptococcus sanguinis type 4 pili subunits. Authors: Shahin, M. / Sheppard, D. / Raynaud, C. / Berry, J.L. / Gurung, I. / Silva, L.M. / Feizi, T. / Liu, Y. / Pelicic, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o5y.cif.gz | 122.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o5y.ent.gz | 96.9 KB | Display | PDB format |
PDBx/mmJSON format | 7o5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o5y_validation.pdf.gz | 459.1 KB | Display | wwPDB validaton report |
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Full document | 7o5y_full_validation.pdf.gz | 467.6 KB | Display | |
Data in XML | 7o5y_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 7o5y_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/7o5y ftp://data.pdbj.org/pub/pdb/validation_reports/o5/7o5y | HTTPS FTP |
-Related structure data
Related structure data | 7oa7C 7oa8C C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15876.808 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sanguinis (bacteria) / Gene: pilA, SSV_2239 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B7GNW3 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.11 Å3/Da / Density % sol: 60.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris pH 8; 0.1 M magnesium nitrate hexahydrate; 23 % (v/v) PEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→93.32 Å / Num. obs: 78394 / % possible obs: 99.75 % / Redundancy: 12.5 % / CC1/2: 0.995 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.77→1.8 Å / Num. unique obs: 3841 / CC1/2: 0.508 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.77→36.92 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 41.75 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→36.92 Å
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Refine LS restraints |
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