+Open data
-Basic information
Entry | Database: PDB / ID: 6wtb | ||||||
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Title | Sort-Tagged Drosophila Cryptochrome | ||||||
Components | Cryptochrome-1 | ||||||
Keywords | CIRCADIAN CLOCK PROTEIN / Flavoprotein / Sortylation Linker | ||||||
Function / homology | Function and homology information UV-A, blue light phototransduction / magnetoreception / detection of light stimulus involved in magnetoreception / gravitaxis / Phosphorylation of PER and TIM / Degradation of CRY / Degradation of TIM / blue light signaling pathway / response to magnetism / response to blue light ...UV-A, blue light phototransduction / magnetoreception / detection of light stimulus involved in magnetoreception / gravitaxis / Phosphorylation of PER and TIM / Degradation of CRY / Degradation of TIM / blue light signaling pathway / response to magnetism / response to blue light / regulation of circadian sleep/wake cycle, sleep / cellular response to light stimulus / blue light photoreceptor activity / entrainment of circadian clock / circadian behavior / entrainment of circadian clock by photoperiod / locomotor rhythm / photoreceptor activity / phototransduction / response to light stimulus / FAD binding / circadian regulation of gene expression / regulation of circadian rhythm / circadian rhythm / flavin adenine dinucleotide binding / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å | ||||||
Authors | Schneps, C.M. / Crane, B.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Commun Biol / Year: 2021 Title: Tuning flavin environment to detect and control light-induced conformational switching in Drosophila cryptochrome. Authors: Chandrasekaran, S. / Schneps, C.M. / Dunleavy, R. / Lin, C. / DeOliveira, C.C. / Ganguly, A. / Crane, B.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wtb.cif.gz | 238.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wtb.ent.gz | 185.4 KB | Display | PDB format |
PDBx/mmJSON format | 6wtb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/6wtb ftp://data.pdbj.org/pub/pdb/validation_reports/wt/6wtb | HTTPS FTP |
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-Related structure data
Related structure data | 4gu5S 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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Unit cell |
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-Components
#1: Protein | Mass: 67602.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cry, CG3772 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): CmpX13 / References: UniProt: O77059 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | The authors state that the cryptochrome has a LPGTG motif encoded on the C-terminus followed by a ...The authors state that the cryptochrome has a LPGTG motif encoded on the C-terminus followed by a GGGGC peptide covalently attached by the enzyme Sortase A. The LPGTG is a molecular recognition site for Sortase A, and the donor peptide is the GGGGC. | |
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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: 2.44 Å3/Da / Density % sol: 50.8 % / Description: Plate-like crystals with slight curvature. |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 4 microliter drop (2 microliter protein solution, 2 microliter well solution) 100 mM Tris (pH 9) 150 mM Magneisum Acetate Tetrahydrate 17% PEG-4000 8 mg/mL sort-tagged WT Drosophila Cryptochrome Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2019 |
Radiation | Monochromator: Cryogenically Cooled Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→39 Å / Num. obs: 39540 / % possible obs: 96.6 % / Redundancy: 3.3 % / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.076 / Rrim(I) all: 0.138 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.58→2.62 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.604 / Num. unique obs: 3882 / CC1/2: 0.795 / CC star: 0.941 / Rpim(I) all: 0.391 / Rrim(I) all: 0.722 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4gu5 Resolution: 2.58→39 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 56.99 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.58→2.67 Å
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