+Open data
-Basic information
Entry | Database: PDB / ID: 1pv6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of lactose permease | ||||||
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: 3.5 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pv6.cif.gz | 162.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pv6.ent.gz | 137.6 KB | Display | PDB format |
PDBx/mmJSON format | 1pv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/1pv6 ftp://data.pdbj.org/pub/pdb/validation_reports/pv/1pv6 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 46484.797 Da / Num. of mol.: 2 / Mutation: C154G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P02920 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 6.45 Å3/Da | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.009 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 28, 2003 |
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→40 Å / Num. all: 31004 / Num. obs: 25733 / % possible obs: 83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 |
Reflection shell | Resolution: 3.5→3.6 Å / % possible all: 71.8 |
Reflection | *PLUS Num. obs: 25917 / % possible obs: 85.9 % / Redundancy: 2.9 % / Num. measured all: 63863 / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS % possible obs: 71.8 % / Rmerge(I) obs: 0.461 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 3.5→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→40 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 3.5 Å / Lowest resolution: 3.6 Å / Rfactor Rfree: 0.379 / Rfactor Rwork: 0.356 |