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- PDB-3kgl: Crystal structure of procruciferin, 11S globulin from Brassica napus -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kgl | ||||||
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Title | Crystal structure of procruciferin, 11S globulin from Brassica napus | ||||||
![]() | Cruciferin | ||||||
![]() | PLANT PROTEIN / procruciferin / 11S seed globulin / Brassica napus / rapeseed / Seed storage protein / Storage protein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tandang-Silvas, M.R. / Mikami, B. / Maruyama, N. / Utsumi, S. | ||||||
![]() | ![]() Title: Conservation and divergence on plant seed 11S globulins based on crystal structures. Authors: Tandang-Silvas, M.R. / Fukuda, T. / Fukuda, C. / Prak, K. / Cabanos, C. / Kimura, A. / Itoh, T. / Mikami, B. / Utsumi, S. / Maruyama, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 467.8 KB | Display | ![]() |
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PDB format | ![]() | 382.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 528.3 KB | Display | ![]() |
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Full document | ![]() | 623.5 KB | Display | |
Data in XML | ![]() | 91 KB | Display | |
Data in CIF | ![]() | 120.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2d5fC ![]() 2d5hC ![]() 2e9qC ![]() 3kscC ![]() 1fxzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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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Unit cell |
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Components
#1: Protein | Mass: 51372.910 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.41 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 32% ammonium sulfate, 0.1M MES pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 29, 2007 / Details: Graphite Monochromator |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.981→50 Å / Num. all: 68497 / Num. obs: 65757 / % possible obs: 96 % / Observed criterion σ(I): 3 / Redundancy: 6.1 % / Biso Wilson estimate: 55.546 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.81 / Num. unique all: 6644 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FXZ Resolution: 2.981→49.787 Å / SU ML: 0.4 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.35 / 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 / Bsol: 39.693 Å2 / ksol: 0.344 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.44 Å2
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Refine analyze | Luzzati coordinate error obs: 0.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.981→49.787 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: 24
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