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Open data
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Basic information
Entry | Database: PDB / ID: 3f4i | ||||||
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Title | Crystal Structure of LeuT bound to L-selenomethionine and sodium | ||||||
![]() | Transporter | ||||||
![]() | TRANSPORT PROTEIN / membrane protein / SLC6 / NSS / sodium-couple / neurotransmitter / transporter / Symport / Transmembrane / Transport | ||||||
Function / homology | Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / plasma membrane / SELENOMETHIONINE / Na(+):neurotransmitter symporter (Snf family)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Singh, S.K. / Piscitelli, C.L. / Yamashita, A. / Gouaux, E. | ||||||
![]() | ![]() Title: A competitive inhibitor traps LeuT in an open-to-out conformation. Authors: Singh, S.K. / Piscitelli, C.L. / Yamashita, A. / Gouaux, E. #1: ![]() Title: Antidepressant binding site in a bacterial homologue of neurotransmitter transporters Authors: Singh, S.K. / Yamashita, A. / Gouaux, E. #2: ![]() Title: Crystal structure of a bacterial homologue of Na(+)/Cl(-)-dependent neurotransmitter transporters Authors: Yamashita, A. / Singh, S.K. / Kawate, T. / Jin, Y. / Gouaux, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.5 KB | Display | ![]() |
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PDB format | ![]() | 90.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3f3aC ![]() 3f3cC ![]() 3f3dC ![]() 3f3eC ![]() 3f48C ![]() 3f4jC ![]() 2a65S 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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Unit cell |
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Components
#1: Protein | Mass: 58077.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-MSE / | ||||
#3: Sugar | ChemComp-BOG / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M HEPES, 0.2M NaCl, 17-22% PEG-MME 550, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2008 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→81.38 Å / Num. obs: 45123 / % possible obs: 99.5 % / Redundancy: 7.4 % / Biso Wilson estimate: 29.62 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.6 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2A65 Resolution: 1.95→31.105 Å / SU ML: 0.2 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 20.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.453 Å2 / ksol: 0.316 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→31.105 Å
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Refine LS restraints |
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LS refinement shell |
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