[English] 日本語
![](img/lk-miru.gif)
- PDB-3de0: Proteinase K by LB nanotemplate method after the second step of h... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3de0 | ||||||
---|---|---|---|---|---|---|---|
Title | Proteinase K by LB nanotemplate method after the second step of high X-Ray dose on ESRF ID23-1 beamline | ||||||
![]() | Proteinase K | ||||||
![]() | HYDROLASE / Alpha and beta proteins / Subtilases / proteinase K / Calcium / Metal-binding / Protease / Serine protease / Zymogen | ||||||
Function / homology | ![]() peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Pechkova, E. / Tripathi, S.K. / Nicolini, C. | ||||||
![]() | ![]() Title: Radiation stability of proteinase K crystals grown by LB nanotemplate method Authors: Pechkova, E. / Tripathi, S. / Ravelli, R.B. / McSweeney, S. / Nicolini, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 67.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 48.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 429.7 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3d9qC ![]() 3ddzSC ![]() 3de1C ![]() 3de2C ![]() 3de3C ![]() 3de4C ![]() 3de5C ![]() 3de6C ![]() 3de7C C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 28930.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.81 % / Mosaicity: 0.4 ° |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20mg/ml of protein in 25mM HEPES, pH7.0, reservoir solution composed by 25mM HEPES and 400mM Na/K tartrate at pH7.0. Onto the siliconized glass cover slides were mixed 4 microL of protein ...Details: 20mg/ml of protein in 25mM HEPES, pH7.0, reservoir solution composed by 25mM HEPES and 400mM Na/K tartrate at pH7.0. Onto the siliconized glass cover slides were mixed 4 microL of protein solution with 4 microL of reservoir solution., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2007 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→56.344 Å / Num. obs: 17199 / % possible obs: 89.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 1.8 / Num. measured all: 12851 / Num. unique all: 2460 / Rsym value: 0.293 / % possible all: 89.3 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3DDZ Resolution: 1.9→34.83 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.883 / SU B: 2.87 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 5.88 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→34.83 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|