[English] 日本語
Yorodumi- PDB-1jv6: BACTERIORHODOPSIN D85S/F219L DOUBLE MUTANT AT 2.00 ANGSTROM RESOLUTION -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jv6 | ||||||
---|---|---|---|---|---|---|---|
Title | BACTERIORHODOPSIN D85S/F219L DOUBLE MUTANT AT 2.00 ANGSTROM RESOLUTION | ||||||
Components | Bacteriorhodopsin | ||||||
Keywords | ION TRANSPORT / PHOTORECEPTOR / HALOARCHAEA / 7-TRANSMEMBRANE / F219L MUTANT / CUBIC LIPID PHASE | ||||||
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: 2 Å | ||||||
Authors | Rouhani, S. / Cartailler, J.-P. / Facciotti, M.T. / Walian, P. / Needleman, R. / Lanyi, J.K. / Glaeser, R.M. / Luecke, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Crystal structure of the D85S mutant of bacteriorhodopsin: model of an O-like photocycle intermediate. Authors: Rouhani, S. / Cartailler, J.P. / Facciotti, M.T. / Walian, P. / Needleman, R. / Lanyi, J.K. / Glaeser, R.M. / Luecke, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jv6.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jv6.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 1jv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/1jv6 ftp://data.pdbj.org/pub/pdb/validation_reports/jv/1jv6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1jv7SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26867.475 Da / Num. of mol.: 1 / Mutation: D85S,F219L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halobacterium salinarum (Halophile) / Gene: Bop / Plasmid: pNov-r / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945 | ||
---|---|---|---|
#2: Chemical | ChemComp-RET / | ||
#3: Chemical | ChemComp-LI1 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.1 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: cubic lipid phase / pH: 5.6 Details: monoolein, octyl-beta-D-glucopyranoside, pH 5.6, cubic lipid phase, temperature 293K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃Details: Landau, E.M., (1996) Proc.Natl.Acad.Sci.USA., 93, 14532. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | |||||||||
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Apr 7, 1999 | |||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 2→30 Å / Num. all: 18717 / Num. obs: 14934 / % possible obs: 79.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Rsym value: 0.077 / Net I/σ(I): 14.4 | |||||||||
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 2.6 / Num. unique all: 769 / Rsym value: 0.558 / % possible all: 42 | |||||||||
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 99 Å / Num. measured all: 152520 / Rmerge(I) obs: 0.077 | |||||||||
Reflection shell | *PLUS % possible obs: 70.8 % / Rmerge(I) obs: 0.558 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JV7 (Bacteriorhodopsin D85S coordinates, without diether lipids nor water) Resolution: 2→12 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber Details: Intensities (I) and not amplitude (F) was used in refinement.
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→12 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top | |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 12 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.222 / Rfactor Rfree: 0.24 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |