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Yorodumi- PDB-8i11: Crystal structure of LOV1 domain of phototropin from Klebsormidiu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i11 | ||||||
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Title | Crystal structure of LOV1 domain of phototropin from Klebsormidium nitens | ||||||
Components | Phototropin | ||||||
Keywords | FLAVOPROTEIN / ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information blue light photoreceptor activity / non-specific serine/threonine protein kinase / phosphorylation / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Klebsormidium nitens (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.855 Å | ||||||
Authors | Gautam, A.K. / Sharma, S. / Gourinath, S. / Kateriya, S. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of LOV1 domain of phototropin from klebsormidium nitens Authors: Gautam, A.K. / Sharma, S. / Gourinath, S. / kateria, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i11.cif.gz | 43.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i11.ent.gz | 27.1 KB | Display | PDB format |
PDBx/mmJSON format | 8i11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/8i11 ftp://data.pdbj.org/pub/pdb/validation_reports/i1/8i11 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17010.318 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsormidium nitens (plant) / Gene: KFL_000480260 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Y1HNG4 |
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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: 2.92 Å3/Da / Density % sol: 57.9 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: magnesium Sulfate hydrate, HEPES sodium pH 7.0, lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8856 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→42.34 Å / Num. obs: 17804 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.99 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.855→5 Å / Num. unique obs: 858 / CC1/2: 0.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.855→42.34 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.105 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.681 Å2
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Refinement step | Cycle: LAST / Resolution: 1.855→42.34 Å
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Refine LS restraints |
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LS refinement shell |
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