+
Open data
-
Basic information
Entry | Database: PDB / ID: 5xty | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of 11S allergen from Cocos nucifera L. | ||||||
![]() | 11S globulin isoform 1 | ||||||
![]() | ALLERGEN / 11S Allergen / cocosin / coconut / twinning | ||||||
Function / homology | ![]() seed maturation / extraorganismal space / seed development / nutrient reservoir activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Vajravijayan, S. / Nandhagopal, N. / Gunasekaran, K. | ||||||
![]() | ![]() Title: Crystal structure determination and analysis of 11S coconut allergen: Cocosin Authors: Vajravijayan, S. / Nandhagopal, N. / Gunasekaran, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 152.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 124.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 502.2 KB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 46.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 52666.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.64 Å3/Da / Density % sol: 25.16 % / Description: Prismatic crystals |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES (pH 7.5), 0.2M Mgcl2 and 10% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection twin | Operator: k,h,-l / Fraction: 0.53 |
Reflection | Resolution: 2.2→31.7 Å / Num. obs: 33993 / % possible obs: 99.7 % / Redundancy: 2.5 % / Rsym value: 0.082 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.2→2.279 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3338 / % possible all: 97.45 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.2→29.833 Å / Cross valid method: FREE R-VALUE / σ(F): 41.51 / Phase error: 35.4 / Stereochemistry target values: TWIN_LSQ_F
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→29.833 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|