[English] 日本語
![](img/lk-miru.gif)
- PDB-6jls: Crystal Structure of FMN-dependent Cysteine Decarboxylases TvaF f... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6jls | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of FMN-dependent Cysteine Decarboxylases TvaF from Thioviridamide Biosynthesis | ||||||
![]() | Putative flavoprotein decarboxylase | ||||||
![]() | BIOSYNTHETIC PROTEIN / FMN-dependent | ||||||
Function / homology | Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / catalytic activity / FLAVIN MONONUCLEOTIDE / Phosphopantothenoylcysteine decarboxylase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, J. / Lu, J. / Wang, H. / Zhu, J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Characterization of the FMN-Dependent Cysteine Decarboxylase from Thioviridamide Biosynthesis. Authors: Lu, J. / Li, J. / Wu, Y. / Fang, X. / Zhu, J. / Wang, H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 80.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 59.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 769 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 769.5 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1g63S S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| x 12||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 20404.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5.23 Å3/Da / Density % sol: 76.51 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: Two micro liters of protein solution containing 7 mg/ml Tvaf in 20 mM Tris, pH 8.0, 50 mM NaCl, was mixed with 2 micro liters of well solution containing 0.1 M Sodium chloride, 0.1M Bicine ...Details: Two micro liters of protein solution containing 7 mg/ml Tvaf in 20 mM Tris, pH 8.0, 50 mM NaCl, was mixed with 2 micro liters of well solution containing 0.1 M Sodium chloride, 0.1M Bicine pH 9.0, and 30% PEG 500 MME (vol/vol). The crystallization drop was incubated against 100 micro liters of well solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→76.691 Å / Num. obs: 21611 / % possible obs: 100 % / Redundancy: 29.8 % / CC1/2: 0.999 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.24→2.31 Å / Num. unique obs: 1937 / CC1/2: 0.395 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1G63 Resolution: 2.24→76.691 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.59 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→76.691 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 83.5922 Å / Origin y: 69.3499 Å / Origin z: 49.3223 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |