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- PDB-6jyf: Structure of light-state marine bacterial chloride importer, NM-R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jyf | |||||||||
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Title | Structure of light-state marine bacterial chloride importer, NM-R3, with Pulse laser (ND-1%) at 140K. | |||||||||
![]() | Chloride pumping rhodopsin | |||||||||
![]() | MEMBRANE PROTEIN / Photo-excitation / Chloride pump / Retinal | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yun, J.H. / Ohki, M. / Park, S.Y. / Lee, W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Pumping mechanism of NM-R3, a light-driven bacterial chloride importer in the rhodopsin family. Authors: Yun, J.H. / Ohki, M. / Park, J.H. / Ishimoto, N. / Sato-Tomita, A. / Lee, W. / Jin, Z. / Tame, J.R.H. / Shibayama, N. / Park, S.Y. / Lee, W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.1 KB | Display | ![]() |
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PDB format | ![]() | 52.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jy6C ![]() 6jy7C ![]() 6jy8C ![]() 6jy9C ![]() 6jyaC ![]() 6jybC ![]() 6jycC ![]() 6jydC ![]() 6jyeC ![]() 5ztkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32913.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-RET / | ||||
#3: Chemical | #4: Chemical | ChemComp-OLA / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.1 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 30% polyethylene glycol dimethyl ether 500, 0.15 M sodium chloride, 0.15M calcium chloride, and 0.1 M MES (pH 6.0) buffer |
-Data collection
Diffraction | Mean temperature: 140 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→34.1 Å / Num. obs: 21264 / % possible obs: 95.9 % / Redundancy: 2.9 % / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2→2.03 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ZTK Resolution: 2.004→34.072 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 19.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.004→34.072 Å
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Refine LS restraints |
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LS refinement shell |
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