+Open data
-Basic information
Entry | Database: PDB / ID: 7ud0 | ||||||
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Title | Room Temperature Drosophila Cryptochrome | ||||||
Components | Cryptochrome-1 | ||||||
Keywords | CIRCADIAN CLOCK PROTEIN / light-sensor | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Schneps, C.M. / Crane, B.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: Room-temperature serial synchrotron crystallography of Drosophila cryptochrome. Authors: Schneps, C.M. / 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 | 7ud0.cif.gz | 230.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ud0.ent.gz | 181.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ud0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ud0_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7ud0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7ud0_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 7ud0_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/7ud0 ftp://data.pdbj.org/pub/pdb/validation_reports/ud/7ud0 | HTTPS FTP |
-Related structure data
Related structure data | 4gu5S S: Starting model for refinement |
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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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 62288.051 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 | 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: 2.66 Å3/Da / Density % sol: 53.75 % |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 8.5 Details: 5 mg/mL twin-strep tagged dCRY (1-539) 100 mM Tris (pH 8.5) 150 mM Magnesium acetate tetrahydrate 18% PEG-4000 Mixed 1:1 in Eppendorf tube; no vortexing |
-Data collection
Diffraction | Mean temperature: 298 K / Ambient temp details: Room Temperature / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.1271 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→19.84 Å / Num. obs: 14881 / % possible obs: 89.8 % / Redundancy: 47.4 % / Biso Wilson estimate: 100.7 Å2 / CC1/2: 0.269 / Rmerge(I) obs: 0.649 / Rrim(I) all: 0.658 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 3.5→3.63 Å / Redundancy: 48.6 % / Rmerge(I) obs: 2.52 / Mean I/σ(I) obs: 2 / Num. unique obs: 1462 / CC1/2: 0.213 / Rrim(I) all: 2.55 / % possible all: 89.1 |
Serial crystallography sample delivery | Method: fixed target |
Serial crystallography sample delivery fixed target | Description: Batch crystallization Sample dehydration prevention: Sealed chips with mylar films Sample holding: chip Sample solvent: 100 mM Tris (pH 8.5), 150 mM Magnesium acetate tetrahydrate, 18% PEG-4000 Sample unit size: 10 µm / Support base: goniometer |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GU5 Resolution: 3.5→19.84 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 99.65 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.63 Å
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