[English] 日本語
![](img/lk-miru.gif)
- PDB-2vhr: Atomic resolution (0.95A) structure of purified thaumatin I grown... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2vhr | ||||||
---|---|---|---|---|---|---|---|
Title | Atomic resolution (0.95A) structure of purified thaumatin I grown in sodium L-tartrate at 4 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 114.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 88.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 451.7 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vhkC ![]() 2vi1C ![]() 2vi2C ![]() 2vi3C ![]() 2vi4C ![]() 2vu6C ![]() 2vu7C ![]() 2wbzC ![]() 1kwn C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE |
---|---|
Crystal grow | Temperature: 277 K / Method: microbatch / pH: 7.1 Details: MICROBATCH METHOD : PROTEIN AT 45 MG/ML IN 10MM SODIUM PHOSPHATE WITH 0.25M SODIUM L-TARTRATE (PH=7.1) AND 10% (V/V) GLYCEROL; CRYSTALS GROWN AT 4 C |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 22, 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: 0.95→20 Å / Num. obs: 154038 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 36.9 |
Reflection shell | Resolution: 0.95→0.97 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KWN ![]() 1kwn Resolution: 0.95→20 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.337 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 11.52 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|