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Open data
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Basic information
Entry | Database: PDB / ID: 8asz | ||||||
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Title | PotF with mutations S87Y and A182D in complex with Agmatine | ||||||
![]() | Putrescine-binding periplasmic protein PotF | ||||||
![]() | TRANSPORT PROTEIN / Periplasmic-binding protein / Agmatine | ||||||
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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 277.1 KB | Display | ![]() |
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PDB format | ![]() | 187 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8at0C ![]() 1a99S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39490.637 Da / Num. of mol.: 1 / Mutation: S87Y, A182D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 371 molecules ![](data/chem/img/AG2.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-AG2 / | ||||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.17 M AmAcetate, 0.085 M NaAcetate pH 4.6, 30% PEG 4000, 15% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: 1.28→37.33 Å / Num. obs: 86290 / % possible obs: 99 % / Redundancy: 7.3 % / Biso Wilson estimate: 17.9 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.026 / Rrim(I) all: 0.07 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.28→1.33 Å / Redundancy: 7.4 % / Rmerge(I) obs: 2.904 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 8427 / CC1/2: 0.28 / CC star: 0.661 / Rpim(I) all: 1.122 / Rrim(I) all: 3.118 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1A99 Resolution: 1.28→37.33 Å / SU ML: 0.1768 / Cross valid method: FREE R-VALUE / Phase error: 23.5132 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.28→37.33 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -0.171500911902 Å / Origin y: -0.00215583332271 Å / Origin z: -11.6754793783 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 27 through 369) |