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- PDB-7qe3: Se-M variant of B-trefoil lectin from Salpingoeca rosetta in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qe3 | ||||||
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Title | Se-M variant of B-trefoil lectin from Salpingoeca rosetta in complex with GalNAc | ||||||
![]() | Sarol-1 | ||||||
![]() | SUGAR BINDING PROTEIN / lectin / GalNAc / b-trefoil / pore forming lectin | ||||||
Function / homology | Ricin B-like lectins / (2S)-hexane-1,2,6-triol / 2-acetamido-2-deoxy-beta-D-galactopyranose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Uncharacterized protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Notova, S. / Varrot, A. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: The choanoflagellate pore-forming lectin SaroL-1 punches holes in cancer cells by targeting the tumor-related glycosphingolipid Gb3. Authors: Notova, S. / Bonnardel, F. / Rosato, F. / Siukstaite, L. / Schwaiger, J. / Lim, J.H. / Bovin, N. / Varrot, A. / Ogawa, Y. / Romer, W. / Lisacek, F. / Imberty, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 833.3 KB | Display | ![]() |
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Full document | ![]() | 843.5 KB | Display | |
Data in XML | ![]() | 30.8 KB | Display | |
Data in CIF | ![]() | 45.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qe4C ![]() 7r55C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 3 molecules AAABBB![](data/chem/img/NGA.gif)
![](data/chem/img/NGA.gif)
#1: Protein | Mass: 39211.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | ChemComp-NGA / | |
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-Non-polymers , 5 types, 458 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/1JW.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/1JW.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | #6: Chemical | ChemComp-PGE / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.03 % / Description: plate |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MOPSO, Bis-Tris pH 6.5, 100 mM AA (Arg, Thr, Lys, His), 45 % precipitant mix 6 Morpheus II-2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2020 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→39.775 Å / Num. obs: 44177 / % possible obs: 99.5 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.072 / Rrim(I) all: 0.12 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 5 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 3 / Num. unique obs: 3794 / CC1/2: 0.852 / Rpim(I) all: 0.383 / Rrim(I) all: 0.634 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.486 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→39.775 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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