+Open data
-Basic information
Entry | Database: PDB / ID: 1pv7 | ||||||||||||
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Title | Crystal structure of lactose permease with TDG | ||||||||||||
Components | Lactose permease | ||||||||||||
Keywords | TRANSPORT PROTEIN / Transport / Sugar transport / Symport / membrane protein | ||||||||||||
Function / homology | Function and homology information lactose:proton symporter activity / lactose transport / carbohydrate:proton symporter activity / lactose binding / organic substance transport / carbohydrate transport / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.6 Å | ||||||||||||
Authors | Abramson, J. / Smirnova, I. / Kasho, V. / Verner, G. / Kaback, H.R. / Iwata, S. | ||||||||||||
Citation | Journal: SCIENCE / Year: 2003 Title: Structure and mechanism of the lactose permease of Escherichia coli Authors: Abramson, J. / Smirnova, I. / Kasho, V. / Verner, G. / Kaback, H.R. / Iwata, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pv7.cif.gz | 166.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pv7.ent.gz | 138.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/1pv7 ftp://data.pdbj.org/pub/pdb/validation_reports/pv/1pv7 | HTTPS FTP |
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-Related 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
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.45 Å3/Da | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.915 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 17, 2003 |
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.915 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→40 Å / Num. all: 28638 / Num. obs: 25917 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 |
Reflection shell | Resolution: 3.6→3.7 Å / % possible all: 85.9 |
Reflection | *PLUS Num. obs: 26017 / Redundancy: 2.6 % / Num. measured all: 67117 / Rmerge(I) obs: 0.128 |
Reflection shell | *PLUS % possible obs: 85.6 % / Rmerge(I) obs: 0.443 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.6→4 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.6→4 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3.6 Å / Lowest resolution: 3.7 Å / Rfactor Rfree: 0.373 / Rfactor Rwork: 0.353 |