[English] 日本語
![](img/lk-miru.gif)
- PDB-4xsa: Determining the Molecular Basis for Starter Unit Selection During... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4xsa | ||||||
---|---|---|---|---|---|---|---|
Title | Determining the Molecular Basis for Starter Unit Selection During Daunorubicin Biosynthesis | ||||||
![]() | Daunorubicin-doxorubicin polyketide synthase | ||||||
![]() | TRANSFERASE / biosynthesis / polyketide / daunorubicin / starter unit | ||||||
Function / homology | ![]() secondary metabolite biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jackson, D.R. / Valentic, T.R. / Tsai, S.C. / Patel, A. / Mohammed, L. / Vasilakis, K. / Wattana-amorn, P. / Long, P.F. / Crump, M.P. / Crosby, J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Determining the Molecular Basis for Starter Unit Selection During Daunorubicin Biosynthesis Authors: Jackson, D.R. / Valentic, T.R. / Tsai, S.C. / Patel, A. / Mohammed, L. / Vasilakis, K. / Wattana-amorn, P. / Long, P.F. / Crump, M.P. / Crosby, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 152.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 117.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 443.3 KB | Display | |
Data in XML | ![]() | 31 KB | Display | |
Data in CIF | ![]() | 46.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xs7C ![]() 4xs9C ![]() 4xsbC ![]() 4xqp S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 39486.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Serine 118 is modified to propionyl-serine / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q54816, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.23 % Description: hexagonal crystals that looked like Monopoly houses |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.18 M sodium citrate, 26% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2013 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 40753 / % possible obs: 99.6 % / Redundancy: 21 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 20.2 % / Rmerge(I) obs: 0.759 / % possible all: 99.2 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 4XQP ![]() 4xqp Resolution: 2.204→45.738 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.6 / 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: 2.204→45.738 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|