[English] 日本語
![](img/lk-miru.gif)
- PDB-6zui: Crystal structure of the Cys-Ser mutant of the cpYFP-based biosen... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6zui | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Cys-Ser mutant of the cpYFP-based biosensor for hypochlorous acid | ||||||
![]() | HTH-type transcriptional repressor NemR,Green fluorescent protein,Green fluorescent protein,HTH-type transcriptional repressor NemR | ||||||
![]() | FLUORESCENT PROTEIN / biosensor / hypohalous acid / cpYFP / yellow fluorescent protein | ||||||
Function / homology | ![]() serine-type endopeptidase inhibitor activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tossounian, M.A. / Van Molle, I. / Messens, J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Hypocrates is a genetically encoded fluorescent biosensor for (pseudo)hypohalous acids and their derivatives. Authors: Kostyuk, A.I. / Tossounian, M.A. / Panova, A.S. / Thauvin, M. / Raevskii, R.I. / Ezerina, D. / Wahni, K. / Van Molle, I. / Sergeeva, A.D. / Vertommen, D. / Gorokhovatsky, A.Y. / Baranov, M.S. ...Authors: Kostyuk, A.I. / Tossounian, M.A. / Panova, A.S. / Thauvin, M. / Raevskii, R.I. / Ezerina, D. / Wahni, K. / Van Molle, I. / Sergeeva, A.D. / Vertommen, D. / Gorokhovatsky, A.Y. / Baranov, M.S. / Vriz, S. / Messens, J. / Bilan, D.S. / Belousov, V.V. #1: ![]() Title: Monitoring oxidative inflammatory processes in live cells and tissue with Hypocrates, a genetically encoded biosensor for hypochlorite Authors: Kostyuk, A.I. / Tossounian, M.A. / Panova, A.S. / Thauvin, M. / Wahni, K. / Van Molle, I. / Raevskii, R.I. / Baranov, M.S. / Vriz, S. / Messens, J. / Bilan, D.S. / Belousov, V.V. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 123.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 76.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 49632.641 Da / Num. of mol.: 1 / Mutation: C353S Source method: isolated from a genetically manipulated source Details: The protein contains a chromophore (CR2 = Gly-Tyr-Gly) within the cpYFP domain.,The protein contains a chromophore (CR2 = Gly-Tyr-Gly) within the cpYFP domain.,The protein contains a ...Details: The protein contains a chromophore (CR2 = Gly-Tyr-Gly) within the cpYFP domain.,The protein contains a chromophore (CR2 = Gly-Tyr-Gly) within the cpYFP domain.,The protein contains a chromophore (CR2 = Gly-Tyr-Gly) within the cpYFP domain.,The protein contains a chromophore (CR2 = Gly-Tyr-Gly) within the cpYFP domain. Source: (gene. exp.) ![]() ![]() ![]() ![]() Strain: K12 / Gene: nemR, ydhM, b1649, JW5874, GFP / Production host: ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.4 % |
---|---|
Crystal grow | Temperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris (0.1 M, pH 8), CaCl2 (0.1 M), MgCl2 (0.1 M) and PE15/4 (15%) Protein concentration:7 mg/mL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980113 Å / Relative weight: 1 |
Reflection | Resolution: 2.09962866868→47.72 Å / Num. obs: 22368 / % possible obs: 83 % / Redundancy: 9.3 % / Biso Wilson estimate: 34.3012936225 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.62 / Num. unique obs: 924 / CC1/2: 0.814 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4YZE, 3O77 Resolution: 2.20008218184→47.7185 Å / SU ML: 0.329732416594 / Cross valid method: FREE R-VALUE / σ(F): 1.33787706633 / Phase error: 31.970318773 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.4430328993 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.20008218184→47.7185 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|