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Yorodumi- PDB-1g28: STRUCTURE OF A FLAVIN-BINDING DOMAIN, LOV2, FROM THE CHIMERIC PHY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g28 | ||||||
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Title | STRUCTURE OF A FLAVIN-BINDING DOMAIN, LOV2, FROM THE CHIMERIC PHYTOCHROME/PHOTOTROPIN PHOTORECEPTOR PHY3 | ||||||
Components | PHY3 PROTEIN | ||||||
Keywords | SIGNALING PROTEIN / ELECTRON TRANSPORT / phototropin / LOV / PAS fold / photoreceptor / flavoprotein / FMN-binding domain / alpha-beta structure | ||||||
Function / homology | Function and homology information blue light photoreceptor activity / detection of visible light / non-specific serine/threonine protein kinase / phosphorylation / 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 / MOLECULAR REPLACEMENT / Resolution: 2.73 Å | ||||||
Authors | Crosson, S. / Moffat, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Structure of a flavin-binding plant photoreceptor domain: insights into light-mediated signal transduction 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 | 1g28.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g28.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 1g28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g28_validation.pdf.gz | 661.8 KB | Display | wwPDB validaton report |
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Full document | 1g28_full_validation.pdf.gz | 677.9 KB | Display | |
Data in XML | 1g28_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1g28_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/1g28 ftp://data.pdbj.org/pub/pdb/validation_reports/g2/1g28 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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 Source: (gene. exp.) Adiantum capillus-veneris (maidenhair fern) Gene: PHY3 / Plasmid: PCAL-NEK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / 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: 3.5 Å3/Da / Density % sol: 64.88 % | ||||||||||||||||||||
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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, temperature 293.0K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 24, 2000 / Details: mirrors |
Radiation | Monochromator: Cu-K-alpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→35.16 Å / Num. all: 17568 / Num. obs: 16249 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.73→2.9 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.443 / % possible all: 86.1 |
Reflection shell | *PLUS % possible obs: 86.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→35.16 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 368490.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.79 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.73→35.16 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.73→2.9 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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