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Open data
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Basic information
Entry | Database: PDB / ID: 7vub | ||||||
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Title | Phloem lectin (PP2) complex with Nitrobenzene | ||||||
![]() | Phloem lectin | ||||||
![]() | SUGAR BINDING PROTEIN / Phloem lectin / chitin-binding lectin / Nitrobenzene complex | ||||||
Function / homology | Phloem protein 2-like / Phloem protein 2 / carbohydrate binding / NITROBENZENE / 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 | ![]() | 140.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 738.3 KB | Display | ![]() |
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Full document | ![]() | 739.6 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vs6SC ![]() 7vwbC ![]() 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: 17639.871 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NBZ / | #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: 2.21 Å3/Da / Density % sol: 44.46 % |
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Crystal grow | Temperature: 295 K / Method: microbatch Details: 1.0 M Ammonium citrate dibasic, 0.1 M Sodium acetate trihydrate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50.97 Å / Num. obs: 2585878 / % possible obs: 100 % / Redundancy: 26.6 % / Biso Wilson estimate: 11.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 2.5 |
Reflection shell | Resolution: 1.2→1.22 Å / Rmerge(I) obs: 1.27 / Num. unique obs: 89698 / CC1/2: 0.85 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7VS6 Resolution: 1.2→50.9 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.04 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: 16.129 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→50.9 Å
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Refine LS restraints |
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LS refinement shell |
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