+Open data
-Basic information
Entry | Database: PDB / ID: 8jh0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the light-driven sodium pump IaNaR | ||||||
Components | Xanthorhodopsin | ||||||
Keywords | METAL TRANSPORT / light-driven sodium pump / MEMBRANE PROTEIN | ||||||
Function / homology | Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / RETINAL / Xanthorhodopsin Function and homology information | ||||||
Biological species | Indibacter alkaliphilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Hashimoto, T. / Kato, K. / Tanaka, Y. / Yao, M. / Kikukawa, T. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Multistep conformational changes leading to the gate opening of light-driven sodium pump rhodopsin. Authors: Sato, Y. / Hashimoto, T. / Kato, K. / Okamura, A. / Hasegawa, K. / Shinone, T. / Tanaka, Y. / Tanaka, Y. / Tsukazaki, T. / Tsukamoto, T. / Demura, M. / Yao, M. / Kikukawa, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8jh0.cif.gz | 116 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8jh0.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 8jh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jh0_validation.pdf.gz | 785.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8jh0_full_validation.pdf.gz | 794.8 KB | Display | |
Data in XML | 8jh0_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 8jh0_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/8jh0 ftp://data.pdbj.org/pub/pdb/validation_reports/jh/8jh0 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32701.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Indibacter alkaliphilus (bacteria) / Gene: A33Q_3728 / Production host: Escherichia coli (E. coli) / References: UniProt: S2D3K4 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 46.32 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.1 / Details: Ammonium Nitrate, sodium citrate, PEG 350 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→50 Å / Num. obs: 15200 / % possible obs: 98.1 % / Redundancy: 6.3 % / CC1/2: 0.999 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.79→2.96 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2189 / CC1/2: 0.803 / % possible all: 89.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→49.14 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.56 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→49.14 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|