+Open data
-Basic information
Entry | Database: PDB / ID: 8asz | ||||||
---|---|---|---|---|---|---|---|
Title | PotF with mutations S87Y and A182D in complex with Agmatine | ||||||
Components | Putrescine-binding periplasmic protein PotF | ||||||
Keywords | TRANSPORT PROTEIN / Periplasmic-binding protein / Agmatine | ||||||
Function / homology | Function and homology information 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 | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å | ||||||
Authors | Kroeger, P. / Shanmugaratnam, S. / Hocker, B. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8asz.cif.gz | 277.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8asz.ent.gz | 187 KB | Display | PDB format |
PDBx/mmJSON format | 8asz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/8asz ftp://data.pdbj.org/pub/pdb/validation_reports/as/8asz | HTTPS FTP |
---|
-Related structure data
Related structure data | 8at0C 1a99S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-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.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: potF, b0854, JW0838 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31133 |
---|
-Non-polymers , 6 types, 371 molecules
#2: Chemical | ChemComp-AG2 / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.81 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -0.171500911902 Å / Origin y: -0.00215583332271 Å / Origin z: -11.6754793783 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: (chain 'A' and resid 27 through 369) |