+
Open data
-
Basic information
Entry | Database: PDB / ID: 8at0 | ||||||
---|---|---|---|---|---|---|---|
Title | PotF with mutation D247K | ||||||
![]() | Putrescine-binding periplasmic protein PotF | ||||||
![]() | TRANSPORT PROTEIN / Periplasmic-binding protein / Non-binding variant | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Kroeger, P. / Shanmugaratnam, S. / Hocker, B. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: A fluorescent biosensor for the visualization of Agmatine Authors: Kroeger, P. / Stiel, A.C. / Stueven, B. / Shanmugaratnam, S. / Schoch, S. / Wachten, D. / Hocker, B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 305.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 236.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 495.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 499.3 KB | Display | |
Data in XML | ![]() | 29.3 KB | Display | |
Data in CIF | ![]() | 41.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8aszC ![]() 1a99S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39184.434 Da / Num. of mol.: 2 / Mutation: D247K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 6 types, 320 molecules ![](data/chem/img/ONT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/JFN.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/JFN.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-JFN / ( #5: Chemical | ChemComp-MLI / | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.99 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 2.4 M AmSO4, 0.1 M Bicine pH 9, 10% Jeffamine M600 pH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2021 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.55 Å / Num. obs: 54785 / % possible obs: 99.9 % / Redundancy: 11 % / Biso Wilson estimate: 39.35 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.057 / Rrim(I) all: 0.19 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 11.5 % / Rmerge(I) obs: 2.98 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5385 / CC1/2: 0.256 / CC star: 0.639 / Rpim(I) all: 0.918 / Rrim(I) all: 3.12 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1A99 Resolution: 2→45.55 Å / SU ML: 0.2648 / Cross valid method: FREE R-VALUE / Phase error: 25.75 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→45.55 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 29 - 369 / Label seq-ID: 1 - 341
|