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Open data
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Basic information
Entry | Database: PDB / ID: 8ad2 | ||||||
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Title | Tobacco lectin Nictaba in complex with triacetylchitotriose | ||||||
![]() | Nictaba | ||||||
![]() | SUGAR BINDING PROTEIN / lectin / jelly-roll / NAG-binding / secreted / nuclear | ||||||
Function / homology | Phloem protein 2-like / Phloem protein 2 / triacetyl-beta-chitotriose / Nictaba![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bloch, Y. / Savvides, S.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The crystal structure of the archetypical Nictaba plant lectin reveals the molecular basis for its carbohydrate-binding properties Authors: Bloch, Y. / Da Silva Osterne, V.J. / Savvides, S.N. / Van Damme, E.J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 585.2 KB | Display | ![]() |
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PDB format | ![]() | 461.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8qmgC 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19141.893 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: N-terminal Met-Gly and are a cloning scar. / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.55 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM ZnAc, 100 mM ZnCl2, 100 mM Bis-Tris pH 7.5, 20 % Medium smear. Soaked and cryoprotected in ML supplemented with 5% (v/v) glycerol, 5% (v/v) ethylene glycol , 5% (v/v) DMSO, 1 mM triacetylchitotriose. |
-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: Aug 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2→60.39 Å / Num. obs: 97998 / % possible obs: 93.4 % / Redundancy: 4.06 % / Biso Wilson estimate: 32.4 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.132 / Net I/σ(I): 8.01 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 3.62 % / Mean I/σ(I) obs: 1.23 / Num. unique obs: 11697 / CC1/2: 0.51 / Rrim(I) all: 1.109 / % possible all: 69.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: apo Resolution: 2→54.22 Å / SU ML: 0.2318 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.0929 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→54.22 Å
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Refine LS restraints |
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LS refinement shell |
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