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Yorodumi- PDB-7oyy: E.coli's putrescine receptor variant PotF/D (4JDF) with mutation ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oyy | ||||||
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Title | E.coli's putrescine receptor variant PotF/D (4JDF) with mutation S247D 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: 1.36 Å | ||||||
Authors | Kroeger, P. / Shanmugaratnam, S. / Hocker, B. | ||||||
Funding support | Germany, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oyy.cif.gz | 278.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oyy.ent.gz | 185.3 KB | Display | PDB format |
PDBx/mmJSON format | 7oyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/7oyy ftp://data.pdbj.org/pub/pdb/validation_reports/oy/7oyy | HTTPS FTP |
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-Related structure data
Related structure data | 7oysC 7oytC 7oyuC 7oyvC 7oywC 7oyxC 7oyzC 1a99S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 39572.695 Da / Num. of mol.: 1 / Mutation: S38T, D39E, S87Y, A182D, 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 |
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-Non-polymers , 6 types, 524 molecules
#2: Chemical | ChemComp-SPD / | ||||||
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#3: Chemical | ChemComp-GOL / | ||||||
#4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
-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: 2.15 Å3/Da / Density % sol: 42.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M MES pH 5, 30% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 7, 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: 1.36→35.15 Å / Num. obs: 73425 / % possible obs: 99.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 14.51 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.068 / Rrim(I) all: 0.184 / Net I/σ(I): 7.58 |
Reflection shell | Resolution: 1.36→1.41 Å / Redundancy: 7.3 % / Rmerge(I) obs: 2.53 / Mean I/σ(I) obs: 0.61 / Num. unique obs: 52254 / CC1/2: 0.28 / CC star: 0.661 / Rpim(I) all: 0.988 / Rrim(I) all: 2.721 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A99 Resolution: 1.36→35.15 Å / SU ML: 0.1875 / Cross valid method: FREE R-VALUE / Phase error: 19.7446 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: 19.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→35.15 Å
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Refine LS restraints |
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LS refinement shell |
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