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- PDB-1jgj: CRYSTAL STRUCTURE OF SENSORY RHODOPSIN II AT 2.4 ANGSTROMS: INSIG... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jgj | ||||||
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Title | CRYSTAL STRUCTURE OF SENSORY RHODOPSIN II AT 2.4 ANGSTROMS: INSIGHTS INTO COLOR TUNING AND TRANSDUCER INTERACTION | ||||||
![]() | SENSORY RHODOPSIN II | ||||||
![]() | SIGNALING PROTEIN / SENSORY RHODOPSIN / MEMBRANE PROTEIN / PHOTOTAXIS RECEPTOR | ||||||
Function / homology | ![]() monoatomic ion channel activity / photoreceptor activity / phototransduction / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Luecke, H. | ||||||
![]() | ![]() Title: Crystal structure of sensory rhodopsin II at 2.4 angstroms: insights into color tuning and transducer interaction. Authors: Luecke, H. / Schobert, B. / Lanyi, J.K. / Spudich, E.N. / Spudich, J.L. #1: ![]() Title: Structure of Bacteriorhodopsin at 1.55 Angstrom Resolution Authors: Luecke, H. / Schobert, B. / Richter, H.T. / Cartailler, J.P. / Lanyi, J.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54 KB | Display | ![]() |
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PDB format | ![]() | 38.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.7 KB | Display | ![]() |
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Full document | ![]() | 468.7 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 9.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1c3wS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23175.479 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Sugar | ChemComp-BOG / |
#3: Chemical | ChemComp-RET / |
#4: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.75 % / Description: USED PROTEIN WITHOUT RETINAL | |||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: cubic lipid phase / pH: 5.3 Details: CUBIC LIPID PHASE WITH MO, PRECIPITANT KCL, pH 5.3, cubic lipid phase, 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 4, 2001 / Details: ID13 |
Radiation | Monochromator: DOUBLE-XTAL MONO / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9755 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 10704 / % possible obs: 92.2 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rsym value: 0.085 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.4→2.44 Å / Rmerge(I) obs: 0.44 / % possible all: 92 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Num. measured all: 80761 / Rmerge(I) obs: 0.095 |
Reflection shell | *PLUS % possible obs: 92 % / Num. unique obs: 520 / Rmerge(I) obs: 0.44 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1C3W Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER, CSD
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.45 Å
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.302 / Rfactor Rwork: 0.29 |