+Open data
-Basic information
Entry | Database: PDB / ID: 3f4j | ||||||
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Title | Crystal structure of LeuT bound to glycine and sodium | ||||||
Components | Transporter | ||||||
Keywords | TRANSPORT PROTEIN / membrane protein / NSS / SLC6 / sodium-coupled / 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 / GLYCINE / Na(+):neurotransmitter symporter (Snf family) Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Singh, S.K. / Piscitelli, C.L. / Yamashita, A. / Gouaux, E. | ||||||
Citation | Journal: Science / Year: 2008 Title: A competitive inhibitor traps LeuT in an open-to-out conformation. Authors: Singh, S.K. / Piscitelli, C.L. / Yamashita, A. / Gouaux, E. #1: Journal: Nature / Year: 2007 Title: Antidepressant binding site in a bacterial homologue of neurotransmitter transporters Authors: Singh, S.K. / Yamashita, A. / Gouaux, E. #2: Journal: Nature / Year: 2005 Title: Crystal structure of a bacterial homologue of a Na(+)/Cl(-)-dependent neurotransmitter transporter Authors: Yamashita, A. / Singh, S.K. / Kawate, T. / Jin, Y. / Gouaux, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f4j.cif.gz | 114.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f4j.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 3f4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/3f4j ftp://data.pdbj.org/pub/pdb/validation_reports/f4/3f4j | HTTPS FTP |
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-Related structure data
Related structure data | 3f3aC 3f3cC 3f3dC 3f3eC 3f48C 3f4iC 2a65S 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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2 |
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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.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: snf, aq_2077 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O67854 | ||||
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#2: Chemical | ChemComp-GLY / | ||||
#3: Sugar | ChemComp-BOG / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M HEPES, 0.4M NaCl, 24-26% 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: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2007 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 33833 / % possible obs: 98.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 38.51 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3083 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2A65 Resolution: 2.15→47.94 Å / SU ML: 0.28 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.22 / 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: 73.752 Å2 / ksol: 0.39 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.25 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→47.94 Å
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Refine LS restraints |
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LS refinement shell |
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