+Open data
-Basic information
Entry | Database: PDB / ID: 7pgy | ||||||
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Title | Structure of light-adapted AsLOV2 wild type | ||||||
Components | NPH1-1 | ||||||
Keywords | SIGNALING PROTEIN / flavin / light-oxygen-voltage / optogenetics / photoreceptor / phototropin | ||||||
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 / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Avena sativa (oats) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å | ||||||
Authors | Gelfert, R. / Weyand, M. / Moeglich, A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Signal transduction in light-oxygen-voltage receptors lacking the active-site glutamine. Authors: Dietler, J. / Gelfert, R. / Kaiser, J. / Borin, V. / Renzl, C. / Pilsl, S. / Ranzani, A.T. / Garcia de Fuentes, A. / Gleichmann, T. / Diensthuber, R.P. / Weyand, M. / Mayer, G. / Schapiro, I. / Moglich, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pgy.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pgy.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pgy_validation.pdf.gz | 1002.9 KB | Display | wwPDB validaton report |
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Full document | 7pgy_full_validation.pdf.gz | 1002.6 KB | Display | |
Data in XML | 7pgy_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 7pgy_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/7pgy ftp://data.pdbj.org/pub/pdb/validation_reports/pg/7pgy | HTTPS FTP |
-Related structure data
Related structure data | 7pgxC 7pgzC 7ph0C 2v0uS S: Starting model for refinement 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
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 16853.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Avena sativa (oats) / Gene: NPH1-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CmpX13 / References: UniProt: O49003 |
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-Non-polymers , 7 types, 210 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Chemical | ChemComp-FMN / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 1.97 Å3/Da / Density % sol: 37.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 0.1 M sodium acetate pH 4.6-5.0, 6-8% (w/v) PEG 4000, 30% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2020 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→42.845 Å / Num. obs: 55866 / % possible obs: 99.2 % / Redundancy: 7 % / CC1/2: 0.999 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.09→1.16 Å / Redundancy: 6.2 % / Num. unique obs: 8789 / CC1/2: 0.45 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2v0u Resolution: 1.09→42.845 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.976 / WRfactor Rfree: 0.145 / WRfactor Rwork: 0.107 / SU B: 2.085 / SU ML: 0.038 / Average fsc free: 0.8499 / Average fsc work: 0.8664 / Cross valid method: FREE R-VALUE / ESU R: 0.034 / ESU R Free: 0.036 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: 16.033 Å2
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Refinement step | Cycle: LAST / Resolution: 1.09→42.845 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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