+Open data
-Basic information
Entry | Database: PDB / ID: 6lf2 | ||||||
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Title | SeviL bound to asialo-GM1 saccharide | ||||||
Components | SeviL | ||||||
Keywords | SUGAR BINDING PROTEIN / trefoil / anti-cancer / apoptosis / mussel | ||||||
Function / homology | Ricin B-like lectins / carbohydrate binding / GM1b/asialo-GM1 oligosaccharide-binding R-type lectin Function and homology information | ||||||
Biological species | Septifer virgatus (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kamata, K. / Ozeki, Y. / Park, S.-Y. / Tame, J.R.H. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Sci Rep / Year: 2020 Title: The structure of SeviL, a GM1b/asialo-GM1 binding R-type lectin from the mussel Mytilisepta virgata. Authors: Kamata, K. / Mizutani, K. / Takahashi, K. / Marchetti, R. / Silipo, A. / Addy, C. / Park, S.Y. / Fujii, Y. / Fujita, H. / Konuma, T. / Ikegami, T. / Ozeki, Y. / Tame, J.R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lf2.cif.gz | 87.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lf2.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 6lf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/6lf2 ftp://data.pdbj.org/pub/pdb/validation_reports/lf/6lf2 | HTTPS FTP |
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-Related structure data
Related structure data | 6lf1SC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15347.116 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Septifer virgatus (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A646QV53*PLUS #2: Polysaccharide | Source method: isolated from a genetically manipulated source #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: 2.11 Å3/Da / Density % sol: 41.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M MIB (sodium malonate dibasic monohydrate, imidazole, boric acid), pH 5.0, 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→43.6 Å / Num. obs: 725030 / % possible obs: 99.7 % / Redundancy: 20.4 % / Biso Wilson estimate: 13.03 Å2 / Rpim(I) all: 0.05 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 1.6→1.627 Å / Num. unique obs: 1780 / Rpim(I) all: 0.426 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LF1 Resolution: 1.6→34.2 Å / SU ML: 0.1764 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.4243
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→34.2 Å
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Refine LS restraints |
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LS refinement shell |
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