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Yorodumi- PDB-1jnu: Photoexcited structure of the plant photoreceptor domain, phy3 LOV2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jnu | ||||||
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Title | Photoexcited structure of the plant photoreceptor domain, phy3 LOV2 | ||||||
Components | PHY3 PROTEIN | ||||||
Keywords | SIGNALING PROTEIN / ELECTRON TRANSPORT / cysteinyl-flavin adduct / photoexcited / PAS / LOV / plant photoreceptor / phototropin / photochemistry / light-driven bond / phy3 | ||||||
Function / homology | Function and homology information detection of visible light / blue light photoreceptor activity / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / regulation of DNA-templated transcription / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Adiantum capillus-veneris (maidenhair fern) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Crosson, S. / Moffat, K. | ||||||
Citation | Journal: Plant Cell / Year: 2002 Title: Photoexcited structure of a plant photoreceptor domain reveals a light-driven molecular switch. Authors: Crosson, S. / Moffat, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jnu.cif.gz | 97.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jnu.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jnu_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1jnu_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1jnu_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 1jnu_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/1jnu ftp://data.pdbj.org/pub/pdb/validation_reports/jn/1jnu | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12181.764 Da / Num. of mol.: 4 Fragment: FMN-BINDING DOMAIN OF CHIMERIC PHYTOCHROME/PHOTOTROPIN PHOTORECEPTOR, LOV3 Source method: isolated from a genetically manipulated source Details: contains a cysteinyl-flavin C(4a) covalent adduct Source: (gene. exp.) Adiantum capillus-veneris (maidenhair fern) Gene: phy3 / Plasmid: pcal-n-ek / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9ZWQ6 #2: Chemical | ChemComp-FMN / #3: Water | ChemComp-HOH / | |
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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: 3.56 Å3/Da / Density % sol: 65.47 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 5000 MME, Tris, Glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 5, 2001 |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→26.8 Å / Num. all: 29191 / Num. obs: 17700 / % possible obs: 87.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 1.65 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1583 / % possible all: 79 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 30 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 79 % / Rmerge(I) obs: 0.19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: phy3 LOV2 dark-state structure Resolution: 2.6→26.8 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 32.69 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→26.8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 30 Å / % reflection Rfree: 7.3 % / Rfactor obs: 0.238 / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.238 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32.7 Å2 | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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