+Open data
-Basic information
Entry | Database: PDB / ID: 8ft5 | ||||||
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Title | Crystal structure of LeuT soaked with Crown-5 | ||||||
Components | Na(+):neurotransmitter symporter (Snf family) | ||||||
Keywords | TRANSPORT PROTEIN / amino acid transporter / anomalous diffraction / element identification / multiple crystals | ||||||
Function / homology | Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / membrane / LEUCINE / Na(+):neurotransmitter symporter (Snf family) Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Karasawa, A. / Liu, H. / Quick, M. / Hendrickson, A.H. / Liu, Q. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be Published Title: Crystallographic characterization of sodium ions in a bacterial leucine/sodium symporter Authors: Karasawa, A. / Liu, H. / Quick, M. / Hendrickson, W.A. / Liu, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ft5.cif.gz | 115 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ft5.ent.gz | 85.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ft5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/8ft5 ftp://data.pdbj.org/pub/pdb/validation_reports/ft/8ft5 | HTTPS FTP |
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-Related structure data
Related structure data | 8ft4C 3gjdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 58318.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: snf / Production host: Escherichia coli (E. coli) / References: UniProt: O67854 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-LEU / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES, pH 7.0, 100 mM sodium chloride, 20-25% PEG550 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 2.479 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.479 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→39.44 Å / Num. obs: 7654 / % possible obs: 98.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 122.34 Å2 / CC1/2: 0.982 / Net I/σ(I): 2.3 |
Reflection shell | Resolution: 3.8→3.936 Å / Num. unique obs: 594 / CC1/2: 0.535 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3GJD Resolution: 3.8→39.44 Å / SU ML: 0.5518 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.7298 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: 124.9 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→39.44 Å
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Refine LS restraints |
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LS refinement shell |
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