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- PDB-7vwb: Phloem lectin (PP2) structure -complex with N-Acetyllactosamine (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vwb | ||||||
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Title | Phloem lectin (PP2) structure -complex with N-Acetyllactosamine (LacNAc) | ||||||
![]() | phloem lectin | ||||||
![]() | SUGAR BINDING PROTEIN / Phloem lectin / chitin-binding lectin | ||||||
Function / homology | Phloem protein 2-like / Phloem protein 2 / carbohydrate binding / N-acetyl-alpha-lactosamine / 17 kDa phloem lectin![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sivaji, N. / Bobbili, K.B. / Suguna, K. / Surolia, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and interactions of the phloem lectin (phloem protein 2) Cus17 from Cucumis sativus. Authors: Sivaji, N. / Bobbili, K.B. / Suguna, K. / Surolia, 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 | ![]() | 83.4 KB | Display | ![]() |
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PDB format | ![]() | 58.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vs6SC ![]() 7vubC ![]() 7w4bC S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 17651.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | #3: Chemical | ChemComp-EDO / | #4: 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: 2.67 Å3/Da / Density % sol: 53.95 % |
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Crystal grow | Temperature: 295 K / Method: microbatch Details: 0.1 M MES monohydrate pH 6.0, 22% v/v Polyethylene glycol 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30.19 Å / Num. obs: 28551 / % possible obs: 98 % / Redundancy: 4 % / CC1/2: 0.97 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.18 / Num. unique obs: 4055 / CC1/2: 0.88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7VS6 Resolution: 1.9→24.896 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.153 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: 13.985 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→24.896 Å
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Refine LS restraints |
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LS refinement shell |
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