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Yorodumi- PDB-3usm: Crystal Structure of LeuT bound to L-selenomethionine in space gr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3usm | ||||||
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Title | Crystal Structure of LeuT bound to L-selenomethionine in space group C2 from lipid bicelles (collected at 1.2 A) | ||||||
Components | Transporter | ||||||
Keywords | TRANSPORT PROTEIN / Leucine transporter | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.008 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 | 3usm.cif.gz | 111.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3usm.ent.gz | 85.6 KB | Display | PDB format |
PDBx/mmJSON format | 3usm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3usm_validation.pdf.gz | 454.4 KB | Display | wwPDB validaton report |
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Full document | 3usm_full_validation.pdf.gz | 460.3 KB | Display | |
Data in XML | 3usm_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 3usm_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/3usm ftp://data.pdbj.org/pub/pdb/validation_reports/us/3usm | HTTPS FTP |
-Related structure data
Related structure data | 3usgC 3usiC 3usjC 3uskC 3uslC 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 , 5 types, 14 molecules
#2: Chemical | #3: Chemical | ChemComp-MSE / | #4: Chemical | ChemComp-PC / | #5: Chemical | ChemComp-IOD / | #6: 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: 3.8 Å3/Da / Density % sol: 67.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 100 mM NaAc, 35% MPD, 10%PEG, 50 mM MgCl2, 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-C / Wavelength: 1.2 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2011 |
Radiation | Monochromator: Cryo-cooled double Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. obs: 17133 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2A65 Resolution: 3.008→37.475 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 23.05 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.01 Å2 / ksol: 0.303 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.008→37.475 Å
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Refine LS restraints |
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LS refinement shell |
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