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Open data
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Basic information
Entry | Database: PDB / ID: 7vcg | ||||||
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Title | Thaumatin protected by alginate gel | ||||||
![]() | Thaumatin I | ||||||
![]() | PLANT PROTEIN / Hydrogel Alginate gel | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Muroyama, H. / Tomoike, F. / Nagae, T. / Okada, T. | ||||||
Funding support | 1items
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![]() | ![]() Title: Post-crystallization protection of protein crystals Authors: Morita, S. / Muroyama, H. / Itabashi, T. / Nagae, T. / Takeuchi, S. / Okada, T. / Tomoike, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.6 KB | Display | ![]() |
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PDB format | ![]() | 72.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.2 KB | Display | ![]() |
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Full document | ![]() | 453.4 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lt5C ![]() 3aldS 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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Unit cell |
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Components
#1: Protein | Mass: 22156.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||
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#2: Chemical | ChemComp-TLA / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.71 % |
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Crystal grow | Temperature: 293 K / Method: counter-diffusion / pH: 7.5 / Details: 1 M sodium tartrate, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 21, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→45.91 Å / Num. obs: 71712 / % possible obs: 100 % / Redundancy: 13.9 % / Biso Wilson estimate: 9.17 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.064 / Rrim(I) all: 0.24 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.937 / Num. unique obs: 7048 / CC1/2: 0.785 / Rpim(I) all: 0.262 / Rrim(I) all: 0.973 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ald Resolution: 1.25→28.97 Å / SU ML: 0.0953 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.1683 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 13.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→28.97 Å
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Refine LS restraints |
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LS refinement shell |
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