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- PDB-3r50: Structure analysis of a wound-inducible lectin ipomoelin from swe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3r50 | ||||||
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Title | Structure analysis of a wound-inducible lectin ipomoelin from sweet potato | ||||||
![]() | Ipomoelin | ||||||
![]() | Carbohydrate-binding protein / beta prism / Carbohydrate/Sugar Binding | ||||||
Function / homology | ![]() defense response to insect / positive regulation of stress-activated MAPK cascade / response to wounding / carbohydrate binding / protein homotetramerization Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, K.L. / Chang, W.C. / Jeng, S.T. / Cheng, Y.S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.4 KB | Display | ![]() |
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PDB format | ![]() | 127.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.2 KB | Display | ![]() |
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Full document | ![]() | 478.7 KB | Display | |
Data in XML | ![]() | 33.3 KB | Display | |
Data in CIF | ![]() | 47.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3r51C ![]() 3r52C ![]() 4ddnC ![]() 1ouwS ![]() 3r53 C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17345.420 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.005 M ferric chloride, 0.05 M sodium citrate, 5% jeffamine M-600 against a reservoir of 0.01 M ferric chloride, 0.1 M sodium citrate, 10% jeffamine M-600, pH 5.6, VAPOR DIFFUSION, HANGING ...Details: 0.005 M ferric chloride, 0.05 M sodium citrate, 5% jeffamine M-600 against a reservoir of 0.01 M ferric chloride, 0.1 M sodium citrate, 10% jeffamine M-600, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2009 / Details: mirrors |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→30 Å / Num. obs: 51599 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.27→2.35 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4.65 / Num. unique all: 5264 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OUW Resolution: 2.27→26.21 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 344672.22 / 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: 29.1792 Å2 / ksol: 0.279667 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.27→26.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.27→2.41 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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