[English] 日本語
![](img/lk-miru.gif)
- PDB-6tyk: Crystal structure of iodotyrosine deiodinase (IYD) in the semiqui... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6tyk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of iodotyrosine deiodinase (IYD) in the semiquinone form bound to FMN and 3-iodo-L-tyrosine | ||||||
![]() | iodotyrosine deiodinase | ||||||
![]() | OXIDOREDUCTASE / flavoprotein / dehalogenase / thermophile / halotyrosine | ||||||
Function / homology | ![]() L-tyrosine binding / iodotyrosine deiodinase / iodotyrosine deiodinase activity / tyrosine metabolic process / thyroid hormone metabolic process / FMN binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sun, Z. / Kavran, J.M. / Rokita, S.E. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure of Tn IYD bound in the semiquinone form bound to FMN and 3-iodo-L-tyrosine Authors: Sun, Z. / Kavran, J.M. / Rokita, S.E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 187.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 147.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 22892.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 49049 / DSM 4359 / NS-E / Gene: CTN_0569 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.08 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium citrate, pH 4.5, 3 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 2, 2019 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→38.02 Å / Num. obs: 80875 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 14.15 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.043 / Rrim(I) all: 0.102 / Net I/σ(I): 8.2 / Num. measured all: 437630 / Scaling rejects: 1422 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.1 Å2 / Biso mean: 20.0256 Å2 / Biso min: 7.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→37.818 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|