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Yorodumi- PDB-5e1r: Crystal structure of pecan (carya illinoinensis) vicilin, a new f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e1r | ||||||
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Title | Crystal structure of pecan (carya illinoinensis) vicilin, a new food allergen | ||||||
Components | 7S vicilin | ||||||
Keywords | ALLERGEN / vicilin / food allergy | ||||||
Function / homology | Function and homology information seed maturation / seed development / nutrient reservoir activity / protein homotrimerization / copper ion binding Similarity search - Function | ||||||
Biological species | Carya illinoinensis (pecan) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å | ||||||
Authors | Zhang, Y.Z. | ||||||
Citation | Journal: J.Agric.Food Chem. / Year: 2016 Title: Identification and Characterization of a New Pecan [Carya illinoinensis (Wangenh.) K. Koch] Allergen, Car i 2. Authors: Zhang, Y. / Lee, B. / Du, W.X. / Lyu, S.C. / Nadeau, K.C. / Grauke, L.J. / Zhang, Y. / Wang, S. / Fan, Y. / Yi, J. / McHugh, T.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e1r.cif.gz | 431.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e1r.ent.gz | 347.2 KB | Display | PDB format |
PDBx/mmJSON format | 5e1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e1r_validation.pdf.gz | 493.8 KB | Display | wwPDB validaton report |
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Full document | 5e1r_full_validation.pdf.gz | 519.3 KB | Display | |
Data in XML | 5e1r_validation.xml.gz | 72.7 KB | Display | |
Data in CIF | 5e1r_validation.cif.gz | 96 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/5e1r ftp://data.pdbj.org/pub/pdb/validation_reports/e1/5e1r | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 49103.621 Da / Num. of mol.: 6 / Fragment: UNP residues 369-792 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carya illinoinensis (pecan) / Gene: pec2a1a, pec3a1a, pec4a1a / Plasmid: pTAP1S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3STU4 #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-MPD / ( #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: 1.88 Å3/Da / Density % sol: 34.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M magnesium acetate tetrahydrate, 0.1M Sodium cacodylat trihydrate 30%(v/v) MPD |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.65→50 Å / Num. obs: 61694 / % possible obs: 92.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.2 / Χ2: 0.996 / Net I/av σ(I): 7.364 / Net I/σ(I): 9.3 / Num. measured all: 422187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.651→46.598 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.31 Å2 / Biso mean: 18.3902 Å2 / Biso min: 0.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.651→46.598 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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