+Open data
-Basic information
Entry | Database: PDB / ID: 1brx | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | BACTERIORHODOPSIN/LIPID COMPLEX | |||||||||
Components | BACTERIORHODOPSIN | |||||||||
Keywords | PROTON PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / LIPIDS / PHOTORECEPTOR / HALOARCHAEA | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Luecke, H. / Richter, H.T. / Lanyi, J. | |||||||||
Citation | Journal: Science / Year: 1998 Title: Proton transfer pathways in bacteriorhodopsin at 2.3 angstrom resolution. Authors: Luecke, H. / Richter, H.T. / Lanyi, J.K. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1brx.cif.gz | 48.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1brx.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 1brx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/1brx ftp://data.pdbj.org/pub/pdb/validation_reports/br/1brx | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26797.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SCHIFF BASE LINKAGE BETWEEN LYS 126 (NZ) AND RET 301 (C15) Source: (gene. exp.) Halobacterium salinarum (Halophile) / Cellular location: PLASMA MEMBRANECell membrane / Organ: PLASMA / Cellular location (production host): CYTOPLASM / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945 |
---|---|
#2: Chemical | ChemComp-RET / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 43.08 % / Description: FLASH-COOLED IN LN2 STREAM | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5.6 / Details: pH 5.6 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. obs: 9769 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 25.6 % / Rsym value: 0.113 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.3→2.34 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.443 / % possible all: 75.9 |
Reflection | *PLUS Num. measured all: 250474 / Rmerge(I) obs: 0.113 |
Reflection shell | *PLUS % possible obs: 75.9 % / Rmerge(I) obs: 0.443 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AT9 AND 2BRD Resolution: 2.3→12 Å / Num. parameters: 6544 / Num. restraintsaints: 6912 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: USED TWIN OPTION, REFINED TWIN RATIO: 0.54/0.46.
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: SWAT | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→12 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 4 / Rfactor all: 0.223 / Rfactor obs: 0.18 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |