[English] 日本語
![](img/lk-miru.gif)
- PDB-4fzr: Crystal Structure of SsfS6, Streptomyces sp. SF2575 glycosyltrans... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4fzr | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of SsfS6, Streptomyces sp. SF2575 glycosyltransferase | ||||||
![]() | SsfS6 | ||||||
![]() | TRANSFERASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NATPRO / Glycosyltransferase | ||||||
Function / homology | ![]() UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, F. / Zhou, M. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro) | ||||||
![]() | ![]() Title: Crystal structure of SsfS6, the putative C-glycosyltransferase involved in SF2575 biosynthesis. Authors: Wang, F. / Zhou, M. / Singh, S. / Yennamalli, R.M. / Bingman, C.A. / Thorson, J.S. / Phillips, G.N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 80.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 62.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 435.3 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 43225.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.16 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: Protein Solution (11.4 mg/ml SsfS6 protein, 50mM Tris pH 8.0) mixed in a 1:1 ratio with the well solution (1.13~1.40 M Sodium phosphate monobasic monohydrate / Potassium phosphate dibasic, ...Details: Protein Solution (11.4 mg/ml SsfS6 protein, 50mM Tris pH 8.0) mixed in a 1:1 ratio with the well solution (1.13~1.40 M Sodium phosphate monobasic monohydrate / Potassium phosphate dibasic, pH 8.2) Cryoprotected with 100% Paratone-N, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. all: 19209 / Num. obs: 19017 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 70.76 Å2 / Rmerge(I) obs: 0.094 / Χ2: 0.923 / Net I/σ(I): 8.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-
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: 133.15 Å2 / Biso mean: 39.7201 Å2 / Biso min: 6.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.397→30.763 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
|