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Yorodumi- PDB-6vs7: Sialic acid binding region of Streptococcus Sanguinis SK1 adhesin -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vs7 | ||||||||||||||||||
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Title | Sialic acid binding region of Streptococcus Sanguinis SK1 adhesin | ||||||||||||||||||
Components | Adhesin | ||||||||||||||||||
Keywords | CELL ADHESION / bacterial adhesion / adhesin / serine rich repeat / streptococcus | ||||||||||||||||||
Biological species | Streptococcus sanguinis SK1 = NCTC 7863 (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||||||||
Authors | Stubbs, H.E. / Iverson, T.M. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Tandem sialoglycan-binding modules in a Streptococcus sanguinis serine-rich repeat adhesin create target dependent avidity effects. Authors: Stubbs, H.E. / Bensing, B.A. / Yamakawa, I. / Sharma, P. / Yu, H. / Chen, X. / Sullam, P.M. / Iverson, T.M. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vs7.cif.gz | 206.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vs7.ent.gz | 158.2 KB | Display | PDB format |
PDBx/mmJSON format | 6vs7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/6vs7 ftp://data.pdbj.org/pub/pdb/validation_reports/vs/6vs7 | HTTPS FTP |
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-Related structure data
Related structure data | 6vt2C 6vu6C 6efcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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
-Protein , 1 types, 2 molecules AE
#1: Protein | Mass: 44457.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sanguinis SK1 = NCTC 7863 (bacteria) Strain: SK1 / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 7 types, 972 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
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-Details
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: 2.96 Å3/Da / Density % sol: 58.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: Protein concentration: 72 mg/mL, Protein buffer: 150 mM NaCl, 20 mM tris pH 7.6, Reservoir solution: 20% (w/v) PEG 3350, 0.2 M MgSO4, 0.01 M SrCl2, Cryoprotectant: 20% (w/v) PEG 3350, 0.2 MM MgSO4, 0.01 M SrCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 70039 / % possible obs: 94.3 % / Redundancy: 5.1 % / CC1/2: 0.91 / Net I/σ(I): 18.12 |
Reflection shell | Resolution: 2→2.07 Å / Num. unique obs: 7006 / CC1/2: 0.706 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EFC Resolution: 2→50 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 35.71 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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