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Yorodumi- PDB-3usg: Crystal structure of LeuT bound to L-leucine in space group C2 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3usg | ||||||
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Title | Crystal structure of LeuT bound to L-leucine in space group C2 from lipid bicelles | ||||||
Components | TransporterTransport protein | ||||||
Keywords | TRANSPORT PROTEIN / Leucine transporter | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 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 | 3usg.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3usg.ent.gz | 87.1 KB | Display | PDB format |
PDBx/mmJSON format | 3usg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/3usg ftp://data.pdbj.org/pub/pdb/validation_reports/us/3usg | HTTPS FTP |
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-Related structure data
Related structure data | 3usiC 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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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 58077.438 Da / Num. of mol.: 1 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 |
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-Non-polymers , 7 types, 70 molecules
#2: Chemical | ChemComp-LEU / | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-UND / | #7: Chemical | ChemComp-PC / | #8: 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: 3.84 Å3/Da / Density % sol: 67.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 100 mM NaAc, 30-35% MPD, 5-10%PEG, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2011 |
Radiation | Monochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 74946 / Num. obs: 29352 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2A65 Resolution: 2.502→36.674 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 25.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.26 Å2 / ksol: 0.32 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.502→36.674 Å
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Refine LS restraints |
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LS refinement shell |
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