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Yorodumi- PDB-8qi9: CrPhotLOV1 dark state structure determined by serial synchrotron ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qi9 | |||||||||||||||
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Title | CrPhotLOV1 dark state structure determined by serial synchrotron crystallography at room temperature | |||||||||||||||
Components | Phototropin | |||||||||||||||
Keywords | FLAVOPROTEIN / PHOTOTROPIN / FLAVIN / ELECTRON TRANSPORT | |||||||||||||||
Function / homology | Function and homology information blue light signaling pathway / blue light photoreceptor activity / protein autophosphorylation / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | |||||||||||||||
Authors | Gotthard, G. / Mous, S. / Weinert, T. / Maia, R.N.A. / James, D. / Dworkowski, F. / Gashi, D. / Antonia, F. / Wang, M. / Panepucci, E. ...Gotthard, G. / Mous, S. / Weinert, T. / Maia, R.N.A. / James, D. / Dworkowski, F. / Gashi, D. / Antonia, F. / Wang, M. / Panepucci, E. / Ozerov, D. / Schertler, G.F.X. / Heberle, J. / Standfuss, J. / Nogly, P. | |||||||||||||||
Funding support | European Union, Switzerland, Poland, 4items
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Citation | Journal: Iucrj / Year: 2024 Title: Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography Authors: Gotthard, G. / Mous, S. / Weinert, T. / Maia, R.N.A. / James, D. / Dworkowski, F. / Gashi, D. / Furrer, A. / Wang, M. / Panepuucci, E. / Ozerov, D. / Schertler, G.F.X. / Heberle, J. / Standfuss, J. / Nogly, P. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qi9.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qi9.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 8qi9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qi9_validation.pdf.gz | 782.2 KB | Display | wwPDB validaton report |
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Full document | 8qi9_full_validation.pdf.gz | 783.1 KB | Display | |
Data in XML | 8qi9_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 8qi9_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/8qi9 ftp://data.pdbj.org/pub/pdb/validation_reports/qi/8qi9 | HTTPS FTP |
-Related structure data
Related structure data | 8qi8C 8qiaC 8qibC 8qifC 8qigC 8qihC 8qiiC 8qikC 8qilC 8qimC 8qinC 8qioC 8qipC 8qiqC 8qirC 8qisC 8qitC 8qiuC 8qivC 8qiwC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15338.354 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PHOT, CHLRE_03g199000v5, CHLREDRAFT_183965 / Production host: Escherichia coli (E. coli) References: UniProt: Q8LPD9, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 70.04 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 6.5 Details: 100 mM sodium cacodylate at pH 6.5 and 1.0 M sodium citrate dibasic trihydrate |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→104.7 Å / Num. obs: 17122 / % possible obs: 99.87 % / Redundancy: 1959.27 % / Biso Wilson estimate: 32.45 Å2 / CC1/2: 1 / CC star: 1 / R split: 0.0584 / Net I/σ(I): 13.25 |
Reflection shell | Resolution: 1.87→1.9 Å / Redundancy: 310.4 % / Mean I/σ(I) obs: 0.73 / Num. unique obs: 1673 / CC1/2: 0.33 / CC star: 0.7 / R split: 1.3435 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→60.77 Å / SU ML: 0.2011 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9646 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: 40.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→60.77 Å
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Refine LS restraints |
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LS refinement shell |
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