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Yorodumi- PDB-8j68: Crystal structure of the LOV1 R60K mutant of Klebsormidium nitens... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j68 | ||||||
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Title | Crystal structure of the LOV1 R60K mutant of Klebsormidium nitens phototropin | ||||||
Components | Phototropin | ||||||
Keywords | FLAVOPROTEIN / flavin binding protein | ||||||
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: 1.845 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 | 8j68.cif.gz | 45.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j68.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 8j68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j68_validation.pdf.gz | 743.8 KB | Display | wwPDB validaton report |
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Full document | 8j68_full_validation.pdf.gz | 744.6 KB | Display | |
Data in XML | 8j68_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 8j68_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/8j68 ftp://data.pdbj.org/pub/pdb/validation_reports/j6/8j68 | HTTPS FTP |
-Related structure data
Related structure data | 8i11C 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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Unit cell |
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-Components
#1: Protein | Mass: 16982.305 Da / Num. of mol.: 1 / Mutation: R60K 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: 2.94 Å3/Da / Density % sol: 58.15 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: sodium phosphate monobasic monohydrate, potassium phosphate dibasic at pH 6.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965459 Å / Relative weight: 1 |
Reflection | Resolution: 1.845→53.905 Å / Num. obs: 15532 / % possible obs: 84.8 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.845→5.005 Å / Num. unique obs: 965 / CC1/2: 0.999 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.845→38.146 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.177 / SU B: 3.142 / SU ML: 0.089 / Average fsc free: 0.9585 / Average fsc work: 0.9736 / Cross valid method: FREE R-VALUE / ESU R: 0.136 / ESU R Free: 0.143 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: 34.307 Å2
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Refinement step | Cycle: LAST / Resolution: 1.845→38.146 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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