+
Open data
-
Basic information
Entry | Database: PDB / ID: 1a99 | ||||||
---|---|---|---|---|---|---|---|
Title | PUTRESCINE RECEPTOR (POTF) FROM E. COLI | ||||||
![]() | PUTRESCINE-BINDING PROTEIN | ||||||
![]() | BINDING PROTEIN / TRANSPORT / PERIPLASMIC PUTRESCINE BINDING PROTEIN (POTF) | ||||||
Function / homology | ![]() putrescine transport / putrescine binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Vassylyev, D.G. / Tomitori, H. / Kashiwagi, K. / Morikawa, K. / Igarashi, K. | ||||||
![]() | ![]() Title: Crystal structure and mutational analysis of the Escherichia coli putrescine receptor. Structural basis for substrate specificity. Authors: Vassylyev, D.G. / Tomitori, H. / Kashiwagi, K. / Morikawa, K. / Igarashi, K. #1: ![]() Title: Crystallization and Preliminary X-Ray Analysis of the Periplasmic Receptor (Potf) of the Putrescine Transport System in Escherichia Coli Authors: Vassylyev, D.G. / Kashiwagi, T. / Tomitori, H. / Kashiwagi, K. / Igarashi, K. / Morikawa, K. #2: ![]() Title: Characteristics of the Operon for a Putrescine Transport System that Maps at 19 Minutes on the Escherichia Coli Chromosome Authors: Pistocchi, R. / Kashiwagi, K. / Miyamoto, S. / Nukui, E. / Sadakata, Y. / Kobayashi, H. / Igarashi, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 276.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 233.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 491.4 KB | Display | |
Data in XML | ![]() | 56.7 KB | Display | |
Data in CIF | ![]() | 79.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||
2 | ![]()
| ||||||||||||||||
3 | ![]()
| ||||||||||||||||
4 | ![]()
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-
Components
#1: Protein | Mass: 38299.391 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PUT / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 60 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5 Details: PROTEIN WAS CRYSTALLIZED FROM 2M AMMONIUM SULFATE, 6% GLYCEROL, 200MM CACODYLATE BUFFER (PH 5), pH 5.0 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging dropDetails: Vassylyev, D.G., (1998) Acta Crystallogr.,Sect.D, 54, 132. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 40 Å2 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. obs: 87495 / % possible obs: 94 % / Num. measured all: 273045 / Rmerge(I) obs: 0.069 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.2→30 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: RESTRAINED / Rms dev Biso : 6.5 Å2 / Rms dev position: 1 Å / Weight Biso : 1 / Weight position: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 90790 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|