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- PDB-7xjd: Crystal structure of bacteriorhodopsin in the ground state by red... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xjd | ||||||
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Title | Crystal structure of bacteriorhodopsin in the ground state by red laser irradiation | ||||||
![]() | Bacteriorhodopsin | ||||||
![]() | PROTON TRANSPORT / proton pump / membrane protein | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Taguchi, S. / Niwa, S. / Takeda, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Detailed analysis of distorted retinal and its interaction with surrounding residues in the K intermediate of bacteriorhodopsin. Authors: Taguchi, S. / Niwa, S. / Dao, H.A. / Tanaka, Y. / Takeda, R. / Fukai, S. / Hasegawa, K. / Takeda, 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 | ![]() | 119.5 KB | Display | ![]() |
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PDB format | ![]() | 95.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.6 MB | Display | ![]() |
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Full document | ![]() | 3.6 MB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zilS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25190.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
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#2: Chemical | ChemComp-RET / | ||||||
#3: Chemical | ChemComp-L2P / #4: Chemical | ChemComp-SQU / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.23 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.6 / Details: MO, 2.0-2.5 M PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 15 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.33→50 Å / Num. obs: 52290 / % possible obs: 99.9 % / Redundancy: 5.807 % / Biso Wilson estimate: 23.988 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.082 / Χ2: 0.823 / Net I/σ(I): 11.04 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ZIL Resolution: 1.33→50 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 167.91 Å2 / Biso mean: 32.9284 Å2 / Biso min: 13.96 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→50 Å
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