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Yorodumi- PDB-3usi: Crystal structure of LeuT bound to L-leucine in space group P2 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3usi | ||||||
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Title | Crystal structure of LeuT bound to L-leucine in space group P2 from lipid bicelles | ||||||
Components | TransporterTransport protein | ||||||
Keywords | TRANSPORT PROTEIN / Leucine transporter | ||||||
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: 3.106 Å | ||||||
Authors | Wang, H. / Elferich, J. / Gouaux, E. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: Structures of LeuT in bicelles define conformation and substrate binding in a membrane-like context. Authors: Wang, H. / Elferich, J. / Gouaux, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3usi.cif.gz | 403.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3usi.ent.gz | 334.7 KB | Display | PDB format |
PDBx/mmJSON format | 3usi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/3usi ftp://data.pdbj.org/pub/pdb/validation_reports/us/3usi | HTTPS FTP |
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-Related structure data
Related structure data | 3usgC 3usjC 3uskC 3uslC 3usmC 3usoC 3uspC 2a65S 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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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 58077.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: snf, aq_2077 / Plasmid: pet16b / Production host: Escherichia coli (E. coli) / References: UniProt: O67854 #2: Chemical | ChemComp-NA / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.66 Å3/Da / Density % sol: 53.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 100mM NaAc, 30% MPD, 10% PEG400, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2011 |
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: 3.1→40 Å / Num. obs: 21407 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.8 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2A65 Resolution: 3.106→38.779 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 26.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.408 Å2 / ksol: 0.314 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.106→38.779 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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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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