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- PDB-2vi1: Atomic resolution (1.04 A) structure of purified thaumatin I grow... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vi1 | ||||||
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Title | Atomic resolution (1.04 A) structure of purified thaumatin I grown in sodium D-tartrate at 22 C. | ||||||
![]() | THAUMATIN-1 | ||||||
![]() | PLANT PROTEIN / KINETICS OF CRYSTALLIZATION / CHIRALITY / TEMPERATURE / MICROBATCH / SWEET PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jakoncic, J. / Asherie, N. / Ginsberg, C. | ||||||
![]() | ![]() Title: Tartrate Chirality Determines Thaumatin Crystal Habit Authors: Asherie, N. / Jakoncic, J. / Ginsberg, C. / Greenbaum, A. / Stojanoff, V. / Hrnjez, B.J. / Blass, S. / Berger, J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.9 KB | Display | ![]() |
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PDB format | ![]() | 83.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2vhkC ![]() 2vhrC ![]() 2vi2C ![]() 2vi3C ![]() 2vi4C ![]() 2vu6C ![]() 2vu7C ![]() 2wbzC ![]() 1kwn C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FROM ARIL COVERING SEEDS / Source: (natural) ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 29.3 % / Description: NONE |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7.1 Details: MICROBATCH METHOD; PROTEIN AT 45 MG/ML IN 10MM SODIUM PHOSPHATE WITH 0.25M SODIUM D-TARTRATE (PH=7.1) AND 10% (V/V) GLYCEROL; CRYSTALS GROWN AT 22 C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 23, 2007 / Details: TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8209 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→20 Å / Num. obs: 93952 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 36.1 |
Reflection shell | Resolution: 1.04→1.06 Å / Redundancy: 6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.2 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KWN ![]() 1kwn Resolution: 1.04→16.72 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.565 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.04→16.72 Å
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Refine LS restraints |
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