[English] 日本語
Yorodumi- PDB-7oyt: E.coli's putrescine receptor variant PotF/D (4JDF) with mutations... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oyt | ||||||
---|---|---|---|---|---|---|---|
Title | E.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D F88L in complex with spermidine | ||||||
Components | Putrescine-binding periplasmic protein PotF | ||||||
Keywords | TRANSPORT PROTEIN / E.coli / Periplasmic binding protein / PotF / Spermidine | ||||||
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 (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Shanmugaratnam, S. / Kroeger, P. / Hocker, B. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Fine-tuning spermidine binding modes in the putrescine binding protein PotF. Authors: Kroger, P. / Shanmugaratnam, S. / Scheib, U. / Hocker, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7oyt.cif.gz | 189.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7oyt.ent.gz | 123 KB | Display | PDB format |
PDBx/mmJSON format | 7oyt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/7oyt ftp://data.pdbj.org/pub/pdb/validation_reports/oy/7oyt | HTTPS FTP |
---|
-Related structure data
Related structure data | 7oysC 7oyuC 7oyvC 7oywC 7oyxC 7oyyC 7oyzC 1a99S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39496.645 Da / Num. of mol.: 1 / Mutation: S38T, S87Y, F88L, A182D, D247S, F276W, L348Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: potF, b0854, JW0838 / Plasmid: pET21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31133 |
---|
-Non-polymers , 8 types, 236 molecules
#2: Chemical | ChemComp-SPD / | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | ChemComp-PGE / | #8: Chemical | ChemComp-CL / | #9: 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: 2.26 Å3/Da / Density % sol: 43.38 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M Sodium acetate pH 4.6, 0.2 M Ammonium acetate, 30% PEG 4000 |
-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 PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2019 |
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: 1.6→39.01 Å / Num. obs: 46390 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 23.16 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.054 / Rrim(I) all: 0.139 / Net I/σ(I): 9.03 |
Reflection shell | Resolution: 1.6→1.68 Å / Redundancy: 6.2 % / Rmerge(I) obs: 2.421 / Mean I/σ(I) obs: 0.66 / Num. unique obs: 26997 / CC1/2: 0.273 / CC star: 0.655 / Rpim(I) all: 1.051 / Rrim(I) all: 2.645 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A99 Resolution: 1.6→39.01 Å / SU ML: 0.238 / Cross valid method: FREE R-VALUE / Phase error: 23.6974 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: 31.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→39.01 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -0.807947340349 Å / Origin y: 0.00105818381567 Å / Origin z: -12.4409711457 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: (chain 'A' and resid 29 through 369) |