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Yorodumi- PDB-4mme: Crystal structure of LeuBAT (delta6 mutant) in complex with mazindol -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mme | ||||||
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Title | Crystal structure of LeuBAT (delta6 mutant) in complex with mazindol | ||||||
Components | Transporter | ||||||
Keywords | TRANSPORT PROTEIN / transporter | ||||||
Function / homology | Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / plasma membrane / Chem-29Q / Na(+):neurotransmitter symporter (Snf family) Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Wang, H. / Gouaux, E. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Structural basis for action by diverse antidepressants on biogenic amine transporters. Authors: Wang, H. / Goehring, A. / Wang, K.H. / Penmatsa, A. / Ressler, R. / Gouaux, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mme.cif.gz | 212.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mme.ent.gz | 170.6 KB | Display | PDB format |
PDBx/mmJSON format | 4mme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/4mme ftp://data.pdbj.org/pub/pdb/validation_reports/mm/4mme | HTTPS FTP |
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-Related structure data
Related structure data | 4mm4C 4mm5C 4mm6C 4mm7C 4mm8C 4mm9C 4mmaC 4mmbC 4mmcC 4mmdC 4mmfC 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 58068.391 Da / Num. of mol.: 2 / Mutation: N21Y, G24D, T254S, S256G, Y265F, I359G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: snf, aq_2077 / Production host: Escherichia coli (E. coli) / References: UniProt: O67854 #2: Chemical | ChemComp-NA / #3: Chemical | #4: Sugar | ChemComp-BOG / #5: 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: 2.94 Å3/Da / Density % sol: 58.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.4 Details: 100 mM glycine (pH9.4), 0.1 M Li2SO4, 29%-31% PEG400, 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: Dec 16, 2012 |
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: 2.5→50 Å / Num. all: 46645 / Num. obs: 46598 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40.985 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 24.92 / Stereochemistry target values: ML Details: THE HIGH REAL SPACE R FOR TWO BOG MOLECULES IS DUE TO WEAK ELECTRON DENSITIES FOR THE MOLECULES
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→40.985 Å
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Refine LS restraints |
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LS refinement shell |
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