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Yorodumi- PDB-7pnc: Dark state structure of Sensory Rhodopsin II solved by serial mil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pnc | ||||||
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Title | Dark state structure of Sensory Rhodopsin II solved by serial millisecond crystallography | ||||||
Components | Sensory rhodopsin-2 | ||||||
Keywords | SIGNALING PROTEIN / SRII / serial millisecond crystallography / sensory rhodopsin / sensory rhodopsin II / SMX / SSX | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | Natronomonas pharaonis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Bosman, R. / Ortolani, G. / Branden, G. / Neutze, R. | ||||||
Funding support | European Union, 1items
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Citation | Journal: To Be Published Title: Structural basis of the prolonged photocycle of Sensory Rhodopsin II revealed by serial millisecond crystallography Authors: Bosman, R. / Ortolani, G. / Branden, G. / Neutze, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pnc.cif.gz | 193.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pnc.ent.gz | 133.3 KB | Display | PDB format |
PDBx/mmJSON format | 7pnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pnc_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 7pnc_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 7pnc_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 7pnc_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/7pnc ftp://data.pdbj.org/pub/pdb/validation_reports/pn/7pnc | HTTPS FTP |
-Related structure data
Related structure data | 8qqoC 1h68S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 9 molecules A
#1: Protein | Mass: 26666.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Natronomonas pharaonis (archaea) / Gene: sop2, sopII / Production host: Escherichia coli (E. coli) / References: UniProt: P42196 |
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#4: Sugar | ChemComp-BOG / |
-Non-polymers , 4 types, 47 molecules
#2: Chemical | ChemComp-RET / | ||||
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#3: Chemical | #5: Chemical | ChemComp-MPG / [( #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.04 % |
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Crystal grow | Temperature: 295 K / Method: lipidic cubic phase Details: CaCl 150mM, Glycine 100mM, 38%(v/v) PEG 400, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0000342 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 15, 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: 2.1→39.44 Å / Num. obs: 18087 / % possible obs: 100 % / Redundancy: 242 % / Biso Wilson estimate: 33.33 Å2 / CC1/2: 0.991 / CC star: 0.998 / R split: 0.1399 / Net I/σ(I): 5.56 |
Reflection shell | Resolution: 2.11→2.14 Å / Num. unique obs: 1722 / CC1/2: 0.31 / CC star: 0.686 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H68 Resolution: 2.2→39.44 Å / SU ML: 0.1991 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5497 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 55.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→39.44 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 33.0000789233 Å / Origin y: 37.184319392 Å / Origin z: 2.1600188139 Å
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Refinement TLS group | Selection details: all |