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- PDB-7oyx: 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: 7oyx | ||||||
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Title | E.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D Y87S F88Y S247D 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 | ![]() | 529.1 KB | Display | ![]() |
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PDB format | ![]() | 365.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 826.6 KB | Display | ![]() |
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Full document | ![]() | 833.2 KB | Display | |
Data in XML | ![]() | 35 KB | Display | |
Data in CIF | ![]() | 55.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oysC ![]() 7oytC ![]() 7oyuC ![]() 7oyvC ![]() 7oywC ![]() 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39498.574 Da / Num. of mol.: 2 / Mutation: S38T, F88Y, A182D, 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 , 8 types, 780 molecules ![](data/chem/img/SPD.gif)
![](data/chem/img/3IE.gif)
![](data/chem/img/4SW.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/4RH.gif)
![](data/chem/img/3IK.gif)
![](data/chem/img/ONT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/3IE.gif)
![](data/chem/img/4SW.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/4RH.gif)
![](data/chem/img/3IK.gif)
![](data/chem/img/ONT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-3IE / ( #4: Chemical | ChemComp-4SW / ( | #5: Chemical | #6: Chemical | ChemComp-4RH / ( | #7: Chemical | ChemComp-3IK / ( | #8: Chemical | ChemComp-ONT / ( | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 49.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 2.4 M AmSO4 + 0.1 M Bicine pH 8.3 + 4.5% Jeffamine M600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 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: 1.37→40.7 Å / Num. obs: 163742 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 16.55 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.061 / Rrim(I) all: 0.166 / Net I/σ(I): 7.21 |
Reflection shell | Resolution: 1.37→1.41 Å / Redundancy: 7.3 % / Rmerge(I) obs: 3.29 / Mean I/σ(I) obs: 0.46 / Num. unique obs: 16029 / CC1/2: 0.24 / CC star: 0.622 / Rpim(I) all: 1.295 / Rrim(I) all: 3.54 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1A99 Resolution: 1.37→40.7 Å / SU ML: 0.2262 / Cross valid method: FREE R-VALUE / Phase error: 24.9749 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: 23.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→40.7 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 29 - 401 / Label seq-ID: 1
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