[English] 日本語
![](img/lk-miru.gif)
- PDB-1pot: SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1pot | ||||||
---|---|---|---|---|---|---|---|
Title | SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (MONOMER FORM) | ||||||
![]() | SPERMIDINE/PUTRESCINE-BINDING PROTEIN | ||||||
![]() | BINDING PROTEIN / POLYAMINE TRANSPORT PROTEIN | ||||||
Function / homology | ![]() spermidine transmembrane transport / spermidine binding / spermidine transport / putrescine transport / putrescine binding / outer membrane-bounded periplasmic space / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Sugiyama, S. / Maenaka, K. / Matsushima, M. / Morikawa, K. | ||||||
![]() | ![]() Title: The 1.8-A X-ray structure of the Escherichia coli PotD protein complexed with spermidine and the mechanism of polyamine binding. Authors: Sugiyama, S. / Matsuo, Y. / Maenaka, K. / Vassylyev, D.G. / Matsushima, M. / Kashiwagi, K. / Igarashi, K. / Morikawa, K. #1: ![]() Title: Crystal Structure of Potd, the Primary Receptor of the Polyamine Transport System in Escherichia Coli Authors: Sugiyama, S. / Vassylyev, D.G. / Matsushima, M. / Kashiwagi, K. / Igarashi, K. / Morikawa, K. #2: ![]() Title: Functions of Pota and Potd Proteins in Spermidine-Preferential Uptake System in Escherichia Coli Authors: Kashiwagi, K. / Miyamoto, S. / Nukui, E. / Kobayashi, H. / Igarashi, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 83 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 62.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 399.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 415.6 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 17 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: 36528.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: THE POLYAMINE TRANSPORT GENES IN ESCHERICHIA COLI HAD BEEN CLONED AND WAS PREVIOUSLY DESCRIBED (KASHIWAGI ET AL., (1990) J.BIOL.CHEM. 265:20893-20897, KASHIWAGI ET AL., (1991) J.BIOL.CHEM. 266:20922-20927) Source: (natural) ![]() ![]() |
---|---|
#2: Chemical | ChemComp-SPD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Wavelength: 1.5418 |
---|---|
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 1, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→300 Å / Num. obs: 24579 / % possible obs: 87.8 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.091 |
Reflection | *PLUS Lowest resolution: 9999 Å / Num. measured all: 246531 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→6 Å / σ(F): 1 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.198 / Rfactor Rwork: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |