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Open data
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Basic information
Entry | Database: PDB / ID: 7u1j | ||||||
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Title | Crystal structure of Pisum sativum convicilin | ||||||
![]() | Convicilin | ||||||
![]() | ALLERGEN / Cupin / Vicilin / Convicilin / Pea / Seed Storage Protein | ||||||
Function / homology | Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Convicilin![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bakestani, I.D. / Robinson, K.A. / Loewen, M.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Pea and lentil 7S globulin crystal structures with comparative immunoglobulin epitope mapping. Authors: Robinson, K.A. / St-Jacques, A.D. / Bakestani, I.D. / Beavington, B.A.G. / Loewen, M.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 419.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456 KB | Display | ![]() |
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Full document | ![]() | 475.8 KB | Display | |
Data in XML | ![]() | 38.4 KB | Display | |
Data in CIF | ![]() | 53.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u1hC ![]() 7u1iC ![]() 1uikS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47440.441 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: Q9M3X6 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.15M Ammonium Acetate, 25% PEG3350, 0.05M Bis Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→134.941 Å / Num. obs: 44137 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.081 / Rrim(I) all: 0.151 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.7→2.81 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.554 / Num. unique obs: 4997 / CC1/2: 0.811 / Rpim(I) all: 0.359 / Rrim(I) all: 0.663 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1UIK Resolution: 2.701→134.941 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.863 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.204 / SU B: 13.705 / SU ML: 0.28 / Average fsc free: 0.8761 / Average fsc work: 0.8982 / Cross valid method: NONE / ESU R: 0.604 / ESU R Free: 0.347 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: 43.743 Å2
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Refinement step | Cycle: LAST / Resolution: 2.701→134.941 Å
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Refine LS restraints |
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LS refinement shell |
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