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- PDB-5vn9: Structure of bacteriorhodopsin from crystals grown at 4 deg C usi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vn9 | ||||||
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Title | Structure of bacteriorhodopsin from crystals grown at 4 deg C using GlyNCOC15+4 as an LCP host lipid | ||||||
![]() | Bacteriorhodopsin | ||||||
![]() | MEMBRANE PROTEIN / 7TM / retinal protein | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ishchenko, A. / Peng, L. / Zinovev, E. / Vlasov, A. / Lee, S.C. / Kuklin, A. / Mishin, A. / Borshchevskiy, V. / Zhang, Q. / Cherezov, V. | ||||||
![]() | ![]() Title: Chemically Stable Lipids for Membrane Protein Crystallization. Authors: Ishchenko, A. / Peng, L. / Zinovev, E. / Vlasov, A. / Lee, S.C. / Kuklin, A. / Mishin, A. / Borshchevskiy, V. / Zhang, Q. / Cherezov, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.9 KB | Display | ![]() |
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PDB format | ![]() | 136.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.1 KB | Display | ![]() |
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Full document | ![]() | 434.6 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vn7C ![]() 1xjiS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28537.510 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700922 / JCM 11081 / NRC-1 / Gene: bop, VNG_1467G / Production host: ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.04 % |
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Crystal grow | Temperature: 277 K / Method: lipidic cubic phase / pH: 5.6 Details: 1.9-3.0 M sodium/potassium phosphate buffer (pH5.6), 3.5% v/v methylpentanediol and 0.5% w/v OG |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→28.342 Å / Num. obs: 15034 / % possible obs: 90 % / Redundancy: 2.7 % / Biso Wilson estimate: 46.5 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.143 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.59→2.69 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1396 / CC1/2: 0.76 / % possible all: 50 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1XJI Resolution: 2.594→28.342 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.87 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.594→28.342 Å
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Refine LS restraints |
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LS refinement shell |
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