+
Open data
-
Basic information
Entry | Database: PDB / ID: 1p8u | ||||||
---|---|---|---|---|---|---|---|
Title | BACTERIORHODOPSIN N' INTERMEDIATE AT 1.62 A RESOLUTION | ||||||
![]() | Bacteriorhodopsin | ||||||
![]() | PROTON TRANSPORT / ION PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / LIPIDS / PHOTORECEPTOR / HALOARCHAEA / 7-TRANSMEMBRANE / SERPENTINE / MEROHEDRAL TWINNING | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lanyi, J.K. | ||||||
![]() | ![]() Title: Crystallographic Structures of the M and N Intermediates of Bacteriorhodopsin: Assembly of a Hydrogen-Bonded Chain of Water Molecules between Asp-96 and the Retinal Schiff Base Authors: Schobert, B. / Brown, L.S. / Lanyi, J.K. | ||||||
History |
| ||||||
Remark 300 | BIOMOLECULE 1 THIS ENTRY IS MADE UP OF TWO MODELS WHICH REPRESENT TWO CONFORMATIONS OF THE WILD- ... BIOMOLECULE 1 THIS ENTRY IS MADE UP OF TWO MODELS WHICH REPRESENT TWO CONFORMATIONS OF THE WILD-TYPE PROTEIN. MODEL 1 IS THE N' INTERMEDIATE WITH OCCUPANCY OF 0.37 WHILE MODEL 2 IS THE NON-ILLUMINATED BACTERIORHODOPSIN (BR STATE) WITH OCCUPANCY OF 0.63. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 119.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 90.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 893.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 959.6 KB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p8hC ![]() 1p8iC ![]() 1m0lS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Number of models | 2 |
-
Components
#1: Protein | Mass: 26901.445 Da / Num. of mol.: 1 / Mutation: V49A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-RET / | ||||
#3: Chemical | ChemComp-LI1 / #4: Chemical | ChemComp-SQU / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.9 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: cubic lipid phase / pH: 5.6 Details: MONO-OLEIN, POTASSIUM PHOSPHATE, pH 5.60, CUBIC LIPID PHASE, temperature 295K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Method: unknown / Details: Gabriele, R., (1998) J. Struct. Biol., 121, 82. | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→25 Å / Num. all: 28071 / Num. obs: 28071 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.05 / Net I/σ(I): 35.7 |
Reflection shell | Resolution: 1.62→1.68 Å / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 3.6 / % possible all: 95.9 |
Reflection | *PLUS Highest resolution: 1.62 Å / Lowest resolution: 25 Å / Num. measured all: 469682 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 95.9 % / Mean I/σ(I) obs: 3.6 |
-
Processing
Software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1M0L Resolution: 1.62→25 Å / Num. parameters: 8321 / Num. restraintsaints: 19772 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||
Refine analyze | Num. disordered residues: 237 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2072.48 | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→25 Å
| |||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.206 / Rfactor Rwork: 0.162 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.62 Å / Lowest resolution: 1.68 Å / Rfactor Rfree: 0.195 / Rfactor Rwork: 0.151 |