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- PDB-7zcm: Dark state structure of Sensory Rhodopsin II in complex with HtrI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zcm | |||||||||
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Title | Dark state structure of Sensory Rhodopsin II in complex with HtrII solved by room temperature serial synchrotron crystallography | |||||||||
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![]() | MEMBRANE PROTEIN / SRII / HtrII / serial synchrotron crystallography / sensory rhodopsin / sensory rhodopsin II / halobacterial transducer II / ssx / signalling protein / TCL | |||||||||
Function / homology | ![]() photoreceptor activity / phototransduction / transmembrane signaling receptor activity / chemotaxis / lysozyme activity / monoatomic ion channel activity / signal transduction / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ortolani, G. / Bosman, R. / Ostojic, L. | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Serial synchrotron crystallography structure of the Sensory rhodopsin II transducer complex Authors: Ortolani, G. / Bosman, R. / Ostojic, L. / Branden, G. / Neutze, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.3 KB | Display | ![]() |
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PDB format | ![]() | 47.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 666 KB | Display | ![]() |
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Full document | ![]() | 677.2 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1h2sS 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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Unit cell |
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Components
#1: Protein | Mass: 24085.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 6317.455 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-RET / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.45 % |
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Crystal grow | Temperature: 295 K / Method: lipidic cubic phase Details: PEG 400 38%, Calcium chloride 0.15 M, Glycine 0.1 M, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0000342 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→27.65 Å / Num. obs: 10066 / % possible obs: 99.54 % / Redundancy: 1.05 % / CC1/2: 0.88 / CC star: 0.96 / Net I/σ(I): 20.73 |
Reflection shell | Resolution: 2.85→2.95 Å / Num. unique obs: 998 / CC1/2: 0.54 |
Serial crystallography sample delivery | Method: injection |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1H2S Resolution: 2.85→27.65 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.15 Å2 / Biso mean: 27.9311 Å2 / Biso min: 1.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.85→27.65 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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