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Yorodumi- PDB-4tpg: Selectivity mechanism of a bacterial homologue of the human drug ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tpg | |||||||||||||||
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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 / complex / secondary active transporter | |||||||||||||||
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 MR-1 (bacteria) synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.91 Å | |||||||||||||||
Authors | Guettou, F. / Quistgaard, E.M. / 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 | 4tpg.cif.gz | 368.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tpg.ent.gz | 306.1 KB | Display | PDB format |
PDBx/mmJSON format | 4tpg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/4tpg ftp://data.pdbj.org/pub/pdb/validation_reports/tp/4tpg | HTTPS FTP |
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-Related structure data
Related structure data | 4tphC 4tpjC 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 MR-1 (bacteria) / Gene: SO_1277 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EHE6 #2: Protein/peptide | | #3: Chemical | ChemComp-ZN / | #4: Sugar | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.05 Å3/Da / Density % sol: 69.61 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M phosphate citrate, 36% PEG300, 0.12 M ZnCl2 / PH range: 4 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / 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: 3.91→4.01 Å / Num. obs: 31871 / % possible obs: 90.6 % / Redundancy: 4.8 % / Net I/σ(I): 7.14 |
Reflection shell | Resolution: 3.91→4.01 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.18 / % possible all: 39.3 |
-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: 3.91→4.01 Å / SU ML: 0.55 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 32.8 / Stereochemistry target values: ML Details: 52.30 percent of collected reflections collected used in refinement. The crystal suffered severe radiation damage and "died" during collection. Authors had to cut the data prior to ...Details: 52.30 percent of collected reflections collected used in refinement. The crystal suffered severe radiation damage and "died" during collection. Authors had to cut the data prior to refinement dues to bad quality. They also used the online anisotropy server (http://services.mbi.ucla.edu/anisoscale/) for data scaling.
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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: 3.91→4.01 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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