+Open data
-Basic information
Entry | Database: PDB / ID: 6ye8 | ||||||
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Title | E.coli's Putrescine receptor PotF complexed with Spermidine | ||||||
Components | Putrescine-binding periplasmic protein | ||||||
Keywords | TRANSPORT PROTEIN / Periplasmic binding protein / E.coli / 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 K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Shanmugaratnam, S. / Kroeger, P. / Hocker, B. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Structure / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ye8.cif.gz | 509.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ye8.ent.gz | 351.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ye8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/6ye8 ftp://data.pdbj.org/pub/pdb/validation_reports/ye/6ye8 | HTTPS FTP |
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-Related structure data
Related structure data | 6ye0C 6ye6C 6ye7C 6yebC 6yecC 6yedC 1a99S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Escherichia coli K-12 (bacteria) / Gene: potF, b0854, JW0838 / Plasmid: pET21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31133 |
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-Non-polymers , 6 types, 613 molecules
#2: Chemical | #3: Chemical | ChemComp-JFN / ( #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.84 % |
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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, 10% Jeffamine M600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 13, 2018 Details: vertically collimating mirror (M1, focus at infinity) |
Radiation | Monochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry and a toroidal mirror (M2) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40.71 Å / Num. obs: 128236 / % possible obs: 99.97 % / Redundancy: 11.5 % / Biso Wilson estimate: 25.35 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.07125 / Rpim(I) all: 0.02191 / Rrim(I) all: 0.07461 / Net I/σ(I): 17.79 |
Reflection shell | Resolution: 1.5→1.554 Å / Redundancy: 11 % / Rmerge(I) obs: 2.663 / Mean I/σ(I) obs: 0.76 / Num. unique obs: 12611 / CC1/2: 0.264 / CC star: 0.647 / Rpim(I) all: 0.8379 / Rrim(I) all: 2.794 / % possible all: 99.99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A99 Resolution: 1.5→40.71 Å / SU ML: 0.1903 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.9395
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→40.71 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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