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Open data
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Basic information
Entry | Database: PDB / ID: 8jz8 | ||||||
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Title | Subatomic structure of orthorhombic thaumatin at 0.89 Angstroms | ||||||
![]() | Thaumatin I | ||||||
![]() | PLANT PROTEIN / Thaumatin / Sweet-tasting protein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Masuda, T. / Suzuki, M. / Yamasaki, M. / Mikami, B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Subatomic structure of orthorhombic thaumatin at 0.89 angstrom reveals that highly flexible conformations are crucial for thaumatin sweetness. Authors: Masuda, T. / Suzuki, M. / Yamasaki, M. / Mikami, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.8 KB | Display | ![]() |
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PDB format | ![]() | 123.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444 KB | Display | ![]() |
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Full document | ![]() | 449.1 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vjqS S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 22228.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M N-(2-acetanido) iminodiacetic acid, 25% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→50 Å / Num. obs: 153640 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.025 / Rrim(I) all: 0.062 / Net I/σ(I): 49.55 |
Reflection shell | Resolution: 0.89→0.91 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 4.81 / Num. unique obs: 7590 / CC1/2: 0.861 / Rpim(I) all: 0.219 / Rrim(I) all: 0.546 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VJQ Resolution: 0.89→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso max: 93.63 Å2 / Biso mean: 12.1813 Å2 / Biso min: 3.66 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.89→20 Å
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LS refinement shell | Resolution: 0.89→0.91 Å
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