[English] 日本語
![](img/lk-miru.gif)
- PDB-3do2: Thermolysin by LB nanotemplate method after high X-Ray dose on ES... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3do2 | ||||||
---|---|---|---|---|---|---|---|
Title | Thermolysin by LB nanotemplate method after high X-Ray dose on ESRF ID14-2 beamline | ||||||
![]() | Thermolysin | ||||||
![]() | HYDROLASE / metalloproteinase / Calcium / Metal-binding / Metalloprotease / Protease / Secreted / Zinc / Zymogen | ||||||
Function / homology | ![]() thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Pechkova, E. / Tripathi, S.K. / 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.K. / Nicolini, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 80.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 59.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 462.8 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dnzSC ![]() 3do0C ![]() 3do1C ![]() 3dvqC ![]() 3dvrC ![]() 3dvsC ![]() 3dw1C ![]() 3dw3C ![]() 3dweC ![]() 3dznC ![]() 3dzpC ![]() 3dzrC ![]() 3e0aC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Non-polymers , 5 types, 192 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/VAL.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/VAL.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-VAL / | #5: Chemical | ChemComp-LYS / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.9 % / Mosaicity: 0.52 ° |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: DMSO, Ammonium sulfate, MES, hanging drop, 293K, pH6.0, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2007 / Details: Toroidal mirror |
Radiation | Monochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.194→80.161 Å / Num. obs: 89247 / % possible obs: 84 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.238 / Rsym value: 0.238 / Net I/σ(I): 2.9 |
Reflection shell | Resolution: 1.18→1.25 Å / Redundancy: 1.3 % / Num. measured all: 6087 / Num. unique all: 4653 / % possible all: 30.8 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3DNZ Resolution: 1.22→68.04 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.802 / SU B: 1.289 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.085 / 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: 51.95 Å2 / Biso mean: 16.835 Å2 / Biso min: 10.05 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.22→68.04 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.219→1.251 Å / Total num. of bins used: 20 /
|