[English] 日本語
![](img/lk-miru.gif)
- PDB-6mkt: Photoactive Yellow Protein with 3-chlorotyrosine substituted at p... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6mkt | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Photoactive Yellow Protein with 3-chlorotyrosine substituted at position 42 | |||||||||
![]() | Photoactive yellow protein | |||||||||
![]() | SIGNALING PROTEIN / chlorinated chromophore / hydrogen bonding network / active site / low-barrier hydrogen bond | |||||||||
Function / homology | ![]() photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Thomson, B.D. / Both, J. / Wu, Y. / Parrish, R.M. / Martinez, T. / Boxer, S.G. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation. Authors: Thomson, B. / Both, J. / Wu, Y. / Parrish, R.M. / Martinez, T.J. / Boxer, S.G. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 42.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 27 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 440.5 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mhiC ![]() 6mhnC ![]() 6mmdC ![]() 1nwzS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 13923.021 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-HC4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.58 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1M sodium chloride, 2.4M ammonium sulfate, pH = 6.0, drops were microseeded |
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX325HE / Detector: CCD / Date: Nov 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.18076 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→50 Å / Num. obs: 13140 / % possible obs: 77.5 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.21→1.23 Å |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1NWZ Resolution: 1.6→32.896 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.93
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→32.896 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|