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Yorodumi- PDB-6kx6: Crystal structure of mouse Cryptochrome 1 in complex with KL101 c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kx6 | ||||||||||||
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Title | Crystal structure of mouse Cryptochrome 1 in complex with KL101 compound | ||||||||||||
Components | Cryptochrome-1 | ||||||||||||
Keywords | CIRCADIAN CLOCK PROTEIN | ||||||||||||
Function / homology | Function and homology information negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / negative regulation of G protein-coupled receptor signaling pathway / lipid storage / regulation of DNA damage checkpoint / response to glucagon / regulation of gluconeogenesis / E-box binding / entrainment of circadian clock by photoperiod ...negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / negative regulation of G protein-coupled receptor signaling pathway / lipid storage / regulation of DNA damage checkpoint / response to glucagon / regulation of gluconeogenesis / E-box binding / entrainment of circadian clock by photoperiod / photoreceptor activity / response to light stimulus / phosphatase binding / signal transduction in response to DNA damage / negative regulation of gluconeogenesis / positive regulation of gluconeogenesis / negative regulation of protein ubiquitination / FAD binding / response to activity / positive regulation of protein ubiquitination / gluconeogenesis / nuclear receptor binding / circadian regulation of gene expression / response to insulin / regulation of circadian rhythm / kinase binding / histone deacetylase binding / circadian rhythm / glucose homeostasis / double-stranded DNA binding / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Miller, S.A. / Aikawa, Y. / Hirota, T. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Nat.Chem.Biol. / Year: 2020 Title: Isoform-selective regulation of mammalian cryptochromes. Authors: Miller, S. / Son, Y.L. / Aikawa, Y. / Makino, E. / Nagai, Y. / Srivastava, A. / Oshima, T. / Sugiyama, A. / Hara, A. / Abe, K. / Hirata, K. / Oishi, S. / Hagihara, S. / Sato, A. / Tama, F. / ...Authors: Miller, S. / Son, Y.L. / Aikawa, Y. / Makino, E. / Nagai, Y. / Srivastava, A. / Oshima, T. / Sugiyama, A. / Hara, A. / Abe, K. / Hirata, K. / Oishi, S. / Hagihara, S. / Sato, A. / Tama, F. / Itami, K. / Kay, S.A. / Hatori, M. / Hirota, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kx6.cif.gz | 445.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kx6.ent.gz | 297.7 KB | Display | PDB format |
PDBx/mmJSON format | 6kx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kx6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6kx6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6kx6_validation.xml.gz | 37.4 KB | Display | |
Data in CIF | 6kx6_validation.cif.gz | 53.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/6kx6 ftp://data.pdbj.org/pub/pdb/validation_reports/kx/6kx6 | HTTPS FTP |
-Related structure data
Related structure data | 6kx4SC 6kx5C 6kx7C 6kx8C 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: 57371.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P97784 #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: 2.75 Å3/Da / Density % sol: 55.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% (w/v) PEG3350, 200 mM NH4Cl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jun 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2→36.92 Å / Num. obs: 81644 / % possible obs: 98 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.39 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.078 / Rrim(I) all: 0.151 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2→2.11 Å / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 11841 / CC1/2: 0.648 / Rpim(I) all: 0.292 / Rrim(I) all: 0.559 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KX4 Resolution: 2→36.34 Å / SU ML: 0.2528 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.081 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: 20.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→36.34 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 |
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