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- PDB-7oyu: E.coli's putrescine receptor variant PotF/D (4JDF) with mutations... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7oyu | ||||||
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Title | E.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D Y87S F88Y in complex with spermidine | ||||||
![]() | Putrescine-binding periplasmic protein PotF | ||||||
![]() | TRANSPORT PROTEIN / E.coli / Periplasmic binding protein / PotF / Spermidine | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Shanmugaratnam, S. / Kroeger, P. / Hocker, B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Fine-tuning spermidine binding modes in the putrescine binding protein PotF. Authors: Kroger, P. / Shanmugaratnam, S. / Scheib, U. / 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 | ![]() | 184.8 KB | Display | ![]() |
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PDB format | ![]() | 120.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 650.3 KB | Display | ![]() |
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Full document | ![]() | 652.1 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oysC ![]() 7oytC ![]() 7oyvC ![]() 7oywC ![]() 7oyxC ![]() 7oyyC ![]() 7oyzC ![]() 1a99S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 39470.566 Da / Num. of mol.: 1 / Mutation: S38T, F88Y, A182D, D247S, F276W, L348Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: potF, b0854, JW0838 / Plasmid: pET21b(+) / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 190 molecules ![](data/chem/img/PGE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SPD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PGE / | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-SPD / | #6: 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: 2.14 Å3/Da / Density % sol: 42.07 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 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: 1.95→46.36 Å / Num. obs: 25021 / % possible obs: 98.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 30.12 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.093 / Rrim(I) all: 0.227 / Net I/σ(I): 6.44 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 5.7 % / Rmerge(I) obs: 2.231 / Mean I/σ(I) obs: 0.79 / Num. unique obs: 14023 / CC1/2: 0.262 / CC star: 0.644 / Rpim(I) all: 0.996 / Rrim(I) all: 2.451 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1A99 Resolution: 1.95→46.36 Å / SU ML: 0.2521 / Cross valid method: FREE R-VALUE / Phase error: 25.0649 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: 35.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→46.36 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: -0.328129966486 Å / Origin y: -0.0287458903317 Å / Origin z: -11.9408554634 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 29 through 369) |