+Open data
-Basic information
Entry | Database: PDB / ID: 4wf0 | ||||||
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Title | Crystal Structure of iLID - an Improved Light-Inducible Dimer | ||||||
Components | NPH1-1 | ||||||
Keywords | FLAVOPROTEIN / light-inducible dimer | ||||||
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: 1.95 Å | ||||||
Authors | Hallett, R. / Williams, T. / Kuhlman, B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins. Authors: Guntas, G. / Hallett, R.A. / Zimmerman, S.P. / Williams, T. / Yumerefendi, H. / Bear, J.E. / Kuhlman, B. #1: Journal: Chem. Biol. / Year: 2012 Title: Designing photoswitchable peptides using the AsLOV2 domain. Authors: Lungu, O.I. / Hallett, R.A. / Choi, E.J. / Aiken, M.J. / Hahn, K.M. / Kuhlman, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wf0.cif.gz | 134.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wf0.ent.gz | 104.5 KB | Display | PDB format |
PDBx/mmJSON format | 4wf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wf0_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4wf0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4wf0_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 4wf0_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/4wf0 ftp://data.pdbj.org/pub/pdb/validation_reports/wf/4wf0 | HTTPS FTP |
-Related structure data
Related structure data | 2v0uS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18287.562 Da / Num. of mol.: 2 / Fragment: UNP residues 405-543 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Avena sativa (oats) / Gene: NPH1-1 / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O49003 #2: Chemical | #3: Chemical | ChemComp-CL / | #4: 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: 2.63 Å3/Da / Density % sol: 53.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Grown in dark for 3 days. Conditions: 100mM TRIS:HCl pH 8.5, 800mM Lithium Chloride, 32% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HS / Detector: CCD / Date: Jan 31, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→80.38 Å / Num. obs: 26353 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 25.37 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2v0u Resolution: 1.95→31.078 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→31.078 Å
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Refine LS restraints |
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LS refinement shell |
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