[English] 日本語
![](img/lk-miru.gif)
- PDB-5t9q: Conformational Sampling Differences across the Arrhenius Plot Bip... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5t9q | ||||||
---|---|---|---|---|---|---|---|
Title | Conformational Sampling Differences across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin | ||||||
![]() | Thermolysin | ||||||
![]() | HYDROLASE / conformational sampling / room temperature / thermolysin / Arrhenius break | ||||||
Function / homology | ![]() thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dong, M. / Bahnson, B.J. | ||||||
![]() | ![]() Title: Conformational Sampling Differences across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin Authors: Dong, M. / Bahnson, B.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 82.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 59.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 457.5 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5t9iC ![]() 5t9kC ![]() 5tacC ![]() 5tadC ![]() 5taeC ![]() 5taiC ![]() 5tajC ![]() 5takC ![]() 3dnzS C: citing same article ( S: Starting model for refinement |
---|---|
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 / Fragment: UNP residues 233-548 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: npr / Production host: ![]() ![]() |
---|
-Non-polymers , 6 types, 149 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/VAL.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/VAL.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-VAL / | #5: Chemical | ChemComp-LYS / | #6: Chemical | ChemComp-PO4 / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.04 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 1.4 M (NH 4 ) 2 SO 4 , 12% glycerol, 100 mM Tris buffer, pH 8.3 |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 20006 / % possible obs: 97.4 % / Redundancy: 7.7 % / Net I/σ(I): 11.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3DNZ Resolution: 2.1→31.927 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.96
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 30.954 Å2 / ksol: 0.329 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→31.927 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|