+Open data
-Basic information
Entry | Database: PDB / ID: 7vs6 | ||||||
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Title | Phloem lectin (PP2) structure -native form | ||||||
Components | 17 kDa phloem lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / Phloem lectin / chitin-binding lectin | ||||||
Function / homology | Phloem protein 2-like / Phloem protein 2 / carbohydrate binding / : / 17 kDa phloem lectin Function and homology information | ||||||
Biological species | Cucumis sativus (cucumber) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Sivaji, N. / Bobbili, K.B. / Suguna, K. / Surolia, A. | ||||||
Funding support | India, 1items
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Citation | Journal: Structure / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vs6.cif.gz | 46.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vs6.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 7vs6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vs6_validation.pdf.gz | 619.1 KB | Display | wwPDB validaton report |
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Full document | 7vs6_full_validation.pdf.gz | 619.5 KB | Display | |
Data in XML | 7vs6_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 7vs6_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/7vs6 ftp://data.pdbj.org/pub/pdb/validation_reports/vs/7vs6 | HTTPS FTP |
-Related structure data
Related structure data | 7vubC 7vwbC 7w4bC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17639.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cucumis sativus (cucumber) / Gene: Lec17-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LK69 |
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#2: Chemical | ChemComp-PT / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.64 % |
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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: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1.5 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45.6 Å / Num. obs: 575252 / % possible obs: 99.9 % / Redundancy: 70.1 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 56.6 |
Reflection shell | Resolution: 2.5→2.6 Å / Rmerge(I) obs: 0.198 / Num. unique obs: 8209 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→45.5 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.877 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.261 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: 18.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→45.5 Å
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Refine LS restraints |
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