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Yorodumi- PDB-1n9n: Crystal structure of the Phot-LOV1 domain from Chlamydomonas rein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n9n | ||||||
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Title | Crystal structure of the Phot-LOV1 domain from Chlamydomonas reinhardtii in illuminated state. Data set of a single crystal. | ||||||
Components | putative blue light receptor | ||||||
Keywords | ELECTRON TRANSPORT / phototropin / flavin | ||||||
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: 2.3 Å | ||||||
Authors | Fedorov, R. / Schlichting, I. / Hartmann, E. / Domratcheva, T. / Fuhrmann, M. / Hegemann, P. | ||||||
Citation | Journal: Biophys.J. / Year: 2003 Title: Crystal structures and molecular mechanism of a light-induced signaling switch: The Phot-LOV1 domain from Chlamydomonas reinhardtii. Authors: Fedorov, R. / Schlichting, I. / Hartmann, E. / Domratcheva, T. / Fuhrmann, M. / Hegemann, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n9n.cif.gz | 37.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n9n.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 1n9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/1n9n ftp://data.pdbj.org/pub/pdb/validation_reports/n9/1n9n | HTTPS FTP |
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-Related structure data
Related structure data | 1n9lC 1n9oC 1g28S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11989.646 Da / Num. of mol.: 1 / Fragment: residues 17-125 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Plasmid: pET16 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8LPE0, UniProt: Q8LPD9*PLUS |
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#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 64.99 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: HEPES, ammonium sulfate, PEG8000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.969 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2001 |
Radiation | Monochromator: channel - cut Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→15 Å / Num. all: 9230 / Num. obs: 9184 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Biso Wilson estimate: 27.3 Å2 / Rsym value: 0.132 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.3→2.4 Å / Mean I/σ(I) obs: 4.6 / Rsym value: 0.431 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 69773 / Rmerge(I) obs: 0.132 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.431 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G28 Resolution: 2.3→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |