[English] 日本語
![](img/lk-miru.gif)
- PDB-3dzn: Thaumatin by LB nanotemplate method before high X-Ray dose on ESR... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3dzn | ||||||
---|---|---|---|---|---|---|---|
Title | Thaumatin by LB nanotemplate method before high X-Ray dose on ESRF ID29 beamline | ||||||
![]() | Thaumatin-1 | ||||||
![]() | PLANT PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tripathi, S. / Pechkova, E. / Nicolini, C. | ||||||
![]() | ![]() Title: Radiation damage in protein structural characterization by Synchrotron Radiation: State of the art and Nanotechnology-based perspective Authors: Pechkova, E. / Tripathi, S. / Nicolini, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 110.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 84.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3dnzC ![]() 3do0C ![]() 3do1C ![]() 3do2C ![]() 3dvqC ![]() 3dvrC ![]() 3dvsC ![]() 3dw1C ![]() 3dw3C ![]() 3dweC ![]() 3dzpC ![]() 3dzrC ![]() 3e0aC ![]() 1rqwS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 22243.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#2: Chemical | ChemComp-TLA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.15 % / Mosaicity: 0.52 ° |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM ADA, 1M Na/K-tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2007 / Details: toroidal mirror |
Radiation | Monochromator: Si 311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.507→53.852 Å / Num. obs: 33163 / % possible obs: 80.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 |
Reflection shell | Resolution: 1.51→1.59 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 5 / Num. measured all: 1603 / Num. unique all: 1268 / Rsym value: 0.151 / % possible all: 22.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1RQW Resolution: 1.51→45.74 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.916 / SU B: 1.979 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.071 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 175.04 Å2 / Biso mean: 20.749 Å2 / Biso min: 7.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→45.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.507→1.546 Å / Total num. of bins used: 20
|