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Yorodumi- PDB-4tpj: Selectivity mechanism of a bacterial homologue of the human drug ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tpj | |||||||||||||||
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Title | Selectivity mechanism of a bacterial homologue of the human drug peptide transporters PepT1 and PepT2 | |||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / secondary active transporter / complex | |||||||||||||||
Function / homology | Function and homology information dipeptide transmembrane transport / tripeptide transmembrane transporter activity / peptide:proton symporter activity / dipeptide transmembrane transporter activity / membrane / identical protein binding Similarity search - Function | |||||||||||||||
Biological species | Shewanella oneidensis (bacteria) Shewanella oneidensis MR-1 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.201 Å | |||||||||||||||
Authors | Guettou, F. / Quistgaard, E. / Raba, M. / Moberg, P. / Low, C. / Nordlund, P. | |||||||||||||||
Funding support | Sweden, Singapore, 4items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2014 Title: Selectivity mechanism of a bacterial homolog of the human drug-peptide transporters PepT1 and PepT2. Authors: Guettou, F. / Quistgaard, E.M. / Raba, M. / Moberg, P. / Low, C. / Nordlund, P. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tpj.cif.gz | 362.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tpj.ent.gz | 298.9 KB | Display | PDB format |
PDBx/mmJSON format | 4tpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/4tpj ftp://data.pdbj.org/pub/pdb/validation_reports/tp/4tpj | HTTPS FTP |
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-Related structure data
Related structure data | 4tpgC 4tphC 4lepS 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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Unit cell |
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-Components
#1: Protein | Mass: 57224.152 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1277 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EHE6 #2: Protein/peptide | Mass: 231.249 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Production host: Escherichia coli (E. coli) #3: Sugar | #4: Chemical | ChemComp-ZN / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M phosphate citrate pH 4.5, 46% PEG300, 0.12M ZnCl2 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 20, 2013 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→47.56 Å / Num. obs: 25529 / % possible obs: 86.9 % / Redundancy: 14.7 % / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 3.2→3.28 Å / Mean I/σ(I) obs: 2.42 / Num. measured obs: 8600 / Num. unique all: 587 / CC1/2: 0.739 / % possible all: 27.3 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LEP Resolution: 3.201→47.558 Å / SU ML: 0.46 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 35.26 / Stereochemistry target values: ML
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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: 3.201→47.558 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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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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