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Yorodumi- PDB-3r52: Structure analysis of a wound-inducible lectin ipomoelin from swe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r52 | ||||||
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Title | Structure analysis of a wound-inducible lectin ipomoelin from sweet potato | ||||||
Components | Ipomoelin | ||||||
Keywords | Carbohydrate-binding protein / beta prism / Carbohydrate/Sugar Binding | ||||||
Function / homology | Function and homology information defense response to insect / positive regulation of stress-activated MAPK cascade / response to wounding / carbohydrate binding / protein homotetramerization Similarity search - Function | ||||||
Biological species | Ipomoea batatas (sweet potato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Liu, K.L. / Chang, W.C. / Jeng, S.T. / Cheng, Y.S. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Ipomoelin, a jacalin-related lectin with a compact tetrameric association and versatile carbohydrate binding properties regulated by its N terminus. Authors: Chang, W.C. / Liu, K.L. / Hsu, F.C. / Jeng, S.T. / Cheng, Y.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r52.cif.gz | 138.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r52.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 3r52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/3r52 ftp://data.pdbj.org/pub/pdb/validation_reports/r5/3r52 | HTTPS FTP |
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-Related structure data
Related structure data | 3r50SC 3r51C 4ddnC 3r53 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17345.420 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ipomoea batatas (sweet potato) / Plasmid: pTZ18UH-IPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P93193 #2: Sugar | ChemComp-GYP / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.67 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.05 M sodium acetate, 0.05 M cadmium chloride, 15% polyethylene glycol 400 (PEG 400) against a reservoir of 0.1 M sodium acetate, 0.1 M cadmium chloride, 30% PEG 400, pH 4.6, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 25, 2009 / Details: mirrors |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 33243 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.28 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3172 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3R50 Resolution: 2.1→25.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 565453.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.5237 Å2 / ksol: 0.353 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→25.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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