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Yorodumi- PDB-2q72: Crystal Structure Analysis of LeuT complexed with L-leucine, sodi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q72 | ||||||
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Title | Crystal Structure Analysis of LeuT complexed with L-leucine, sodium, and imipramine | ||||||
Components | Transporter | ||||||
Keywords | TRANSPORT PROTEIN / membrane protein / neurotransmitter sodium symporter / occluded / tricyclic antidepressant | ||||||
Function / homology | Function and homology information nitrogen compound transport / sodium ion transmembrane transport / plasma membrane Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Singh, S.K. / Yamashita, A. / Gouaux, E. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Antidepressant binding site in a bacterial homologue of neurotransmitter transporters. Authors: Singh, S.K. / Yamashita, A. / Gouaux, E. #1: Journal: Nature / Year: 2005 Title: Crystal Structure of a Bacterial Homologue of Na+/Cl--dependent neurotransmitter transporters Authors: Yamashita, A. / Singh, S.K. / Kawate, T. / Jin, Y. / Gouaux, E. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 The biological assembly might not be physiologically relevant mainly because of the ...BIOMOLECULE: 1 The biological assembly might not be physiologically relevant mainly because of the results authors obtained in solution. The actual residues in the relevant transmembrane domains (TM9 and TM12) are not conserved in the eukaryotic homologues. Authors are not 100% sure because crosslinking the protein in a lipid bilayer has not been performed. | ||||||
Remark 600 | HETEROGEN The authors state that C2 numbering is in crystallographic notation and it is the same as ...HETEROGEN The authors state that C2 numbering is in crystallographic notation and it is the same as C3 numbering in IUPAC. Regarding the bond order difference for the C5-C6 bond, the authors used the topology and parameter files derived from the small molecule crystal structures of clomipramine and imipramine rather than theoretical values. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q72.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q72.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 2q72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q72_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2q72_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2q72_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 2q72_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/2q72 ftp://data.pdbj.org/pub/pdb/validation_reports/q7/2q72 | HTTPS FTP |
-Related structure data
Related structure data | 2q6hC 2qb4C 2qeiC 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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1 |
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2 |
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Unit cell |
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Details | The biological unit is the monomer, which is the asymmetric unit. A crystallographic dimer can be generated, but its physiological relevance is not yet known. |
-Components
-Protein / Sugars , 2 types, 6 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) / Strain: VF5 / Gene: snf / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O67854 |
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#2: Sugar | ChemComp-BOG / |
-Non-polymers , 4 types, 151 molecules
#3: Chemical | #4: Chemical | ChemComp-LEU / | #5: Chemical | #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: 2.65 Å3/Da / Density % sol: 53.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 17-22% PEGMME 550, 200 mM NaCl, 100 mM HEPES-NaOH, 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: NSLS / Beamline: X29A / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2005 / Details: vertical focusing mirror |
Radiation | Monochromator: channel-cut Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 63941 / Num. obs: 65969 / % possible obs: 95.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 1.93 / Num. unique all: 4839 / % possible all: 73 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2A65 Resolution: 1.7→27.43 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1770346.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 81.4929 Å2 / ksol: 0.397959 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→27.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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