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Open data
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Basic information
Entry | Database: PDB / ID: 6yeb | ||||||
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Title | E.coli's Putrescine receptor PotF in its closed apo state | ||||||
![]() | Putrescine-binding periplasmic protein | ||||||
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Function / homology | ![]() putrescine transport / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shanmugaratnam, S. / Kroeger, P. / Hocker, B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A comprehensive binding study illustrates ligand recognition in the periplasmic binding protein PotF. Authors: Kroger, P. / Shanmugaratnam, S. / Ferruz, N. / Schweimer, K. / 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 | ![]() | 336.9 KB | Display | ![]() |
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PDB format | ![]() | 237.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ye0C ![]() 6ye6C ![]() 6ye7C ![]() 6ye8C ![]() 6yecC ![]() 6yedC ![]() 1a99S C: citing same article ( S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39370.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 290 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / ![]() | ||||||||
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#3: Chemical | ChemComp-PGE / ![]() | ||||||||
#4: Chemical | ChemComp-PEG / ![]() #5: Chemical | ChemComp-EDO / ![]() #6: Chemical | ![]() #7: Chemical | ![]() #8: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.3 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 2.4 M Ammoniumsulfate, 0.1 M Bicine pH 8.8, 5% PEG 3550 |
-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: Jan 17, 2018 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.97→45.68 Å / Num. obs: 58117 / % possible obs: 99.95 % / Redundancy: 10.9 % / Biso Wilson estimate: 44.59 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1242 / Rpim(I) all: 0.0393 / Rrim(I) all: 0.1304 / Net I/σ(I): 12.16 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 11.3 % / Rmerge(I) obs: 3.324 / Mean I/σ(I) obs: 0.68 / Num. unique obs: 5691 / CC1/2: 0.23 / CC star: 0.611 / Rpim(I) all: 1.021 / Rrim(I) all: 3.48 / % possible all: 99.93 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1A99 Resolution: 1.97→45.68 Å / SU ML: 0.2248 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6066
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→45.68 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 |
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