+Open data
-Basic information
Entry | Database: PDB / ID: 1m0l | ||||||
---|---|---|---|---|---|---|---|
Title | BACTERIORHODOPSIN/LIPID COMPLEX AT 1.47 A RESOLUTION | ||||||
Components | BACTERIORHODOPSIN | ||||||
Keywords | ION TRANSPORT / ION PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / LIPIDS / PHOTORECEPTOR / HALOARCHAEA / 7-TRANSMEMBRANE / SERPENTINE / MEROHEDRAL TWINNING | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | Halobacterium salinarum (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Lanyi, J.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal. Authors: Schobert, B. / Cupp-Vickery, J. / Hornak, V. / Smith, S. / Lanyi, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1m0l.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1m0l.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 1m0l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/1m0l ftp://data.pdbj.org/pub/pdb/validation_reports/m0/1m0l | HTTPS FTP |
---|
-Related structure data
Related structure data | 1m0kC 1c3wS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28270.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halobacterium salinarum (Halophile) / Plasmid: prn2367 / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-LI1 / #3: Chemical | ChemComp-SQU / | #4: Chemical | ChemComp-RET / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 41.29 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: cubic lipid phase / pH: 5.6 Details: CUBIC LIPID PHASE WITH MONO-OLEIN, PRECIPITANT PHOSPHATE, pH 5.60, temperature 295K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.6 Details: Landau, E.M., (1996) Proc.Natl.Acad.Sci.USA., 93, 14532. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Aug 20, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→25 Å / Num. obs: 38667 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.039 / Net I/σ(I): 35.5 |
Reflection shell | Resolution: 1.47→1.51 Å / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.9 / % possible all: 92.5 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 599134 / Rmerge(I) obs: 0.039 |
Reflection shell | *PLUS % possible obs: 92.5 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C3W Resolution: 1.47→25 Å / Num. parameters: 8296 / Num. restraintsaints: 8154 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: MEROHEDRAL TWINNING RATIO OF 54/46
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2073 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→25 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 38646 / % reflection Rfree: 5 % / Rfactor all: 0.1488 / Rfactor Rfree: 0.179 / Rfactor Rwork: 0.149 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.47 Å / Lowest resolution: 1.51 Å / Rfactor Rfree: 0.165 / Rfactor Rwork: 0.136 |