[English] 日本語
![](img/lk-miru.gif)
- PDB-1bm1: CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN THE LIGHT-ADAPTED STATE -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1bm1 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN THE LIGHT-ADAPTED STATE | |||||||||
![]() | BACTERIORHODOPSIN | |||||||||
![]() | PHOTORECEPTOR / PROTON PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN | |||||||||
Function / homology | ![]() photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sato, H. / Takeda, K. / Tani, K. / Hino, T. / Okada, T. / Nakasako, M. / Kamiya, N. / Kouyama, T. | |||||||||
![]() | ![]() Title: Specific lipid-protein interactions in a novel honeycomb lattice structure of bacteriorhodopsin. Authors: Sato, H. / Takeda, K. / Tani, K. / Hino, T. / Okada, T. / Nakasako, M. / Kamiya, N. / Kouyama, T. #1: ![]() Title: A Novel Three-Dimensional Crystal of Bacteriorhodopsin Obtained by Successive Fusion of the Vesicular Assemblies Authors: Takeda, K. / Sato, H. / Hino, T. / Kono, M. / Fukuda, K. / Sakurai, I. / Okada, T. / Kouyama, T. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 46.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 35.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 487.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 497.2 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2brdS S: Starting model for refinement |
---|---|
Similar 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 natural source / Source: (natural) ![]() |
---|---|
#2: Chemical | ChemComp-RET / |
#3: Chemical | ChemComp-DPG / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.47 % Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5.2 / Details: pH 5.2 | |||||||||||||||
Crystal grow | *PLUS Temperature: 278 K / Method: vapor diffusion | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 285 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Nov 14, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.012 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 4000 / % possible obs: 80.2 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 |
Reflection shell | Resolution: 3.5→3.65 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.159 / Rsym value: 0.159 / % possible all: 45.2 |
Reflection shell | *PLUS % possible obs: 45.2 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BRD Resolution: 3.5→8 Å / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.269 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.361 / Num. reflection obs: 247 / Rfactor obs: 0.272 |