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Yorodumi- PDB-7ej9: Alternative crystal structure of mouse Cryptochrome 2 in complex ... -
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-Basic information
Entry | Database: PDB / ID: 7ej9 | ||||||
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Title | Alternative crystal structure of mouse Cryptochrome 2 in complex with TH301 compound | ||||||
Components | Cryptochrome-2 | ||||||
Keywords | CIRCADIAN CLOCK PROTEIN / CRY / CRY2 / cryptochrome / PHR | ||||||
Function / homology | Function and homology information regulation of sodium-dependent phosphate transport / negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / lipid storage / entrainment of circadian clock by photoperiod / photoreceptor activity / response to light stimulus / phosphatase binding / FAD binding ...regulation of sodium-dependent phosphate transport / negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / lipid storage / entrainment of circadian clock by photoperiod / photoreceptor activity / response to light stimulus / phosphatase binding / FAD binding / response to activity / nuclear receptor binding / circadian regulation of gene expression / response to insulin / regulation of circadian rhythm / kinase binding / circadian rhythm / protein import into nucleus / glucose homeostasis / single-stranded DNA binding / damaged DNA binding / transcription cis-regulatory region binding / nuclear speck / negative regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / extracellular region / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Miller, S.A. / Hirota, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Structural differences in the FAD-binding pockets and lid loops of mammalian CRY1 and CRY2 for isoform-selective regulation. Authors: Miller, S. / Srivastava, A. / Nagai, Y. / Aikawa, Y. / Tama, F. / Hirota, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ej9.cif.gz | 449.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ej9.ent.gz | 304.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ej9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ej9_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7ej9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7ej9_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 7ej9_validation.cif.gz | 47.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/7ej9 ftp://data.pdbj.org/pub/pdb/validation_reports/ej/7ej9 | HTTPS FTP |
-Related structure data
Related structure data | 7d0mC 7d0nC 7dliC 6kx8S S: Starting model for refinement C: citing same article (ref.) |
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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: 58847.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry2, Kiaa0658 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9R194 #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.29 Å3/Da / Density % sol: 46.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M HEPES-NaOH pH 7.0, 0.35 M NaCl, 18% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→57.7 Å / Num. obs: 33745 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 38.52 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.07 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4832 / CC1/2: 0.807 / Rpim(I) all: 0.34 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KX8 Resolution: 2.6→53.02 Å / SU ML: 0.3379 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7735 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→53.02 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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