+Open data
-Basic information
Entry | Database: PDB / ID: 4i6e | ||||||
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Title | A vertebrate cryptochrome | ||||||
Components | Cryptochrome-2 | ||||||
Keywords | TRANSCRIPTION / Cryptochrome Circadian Clock / Photolyase fold / Circadian Clock / FAD / Nucleus | ||||||
Function / homology | Function and homology information regulation of sodium-dependent phosphate transport / Cry-Per complex / 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 ...regulation of sodium-dependent phosphate transport / Cry-Per complex / 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 / regulation of circadian rhythm / kinase binding / circadian regulation of gene expression / response to insulin / circadian rhythm / protein import into nucleus / glucose homeostasis / single-stranded DNA binding / transcription cis-regulatory region binding / damaged DNA 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: 2.7 Å | ||||||
Authors | Xing, W. / Busino, L. / Hinds, T.R. / Marionni, S.T. / Saifee, N.H. / Bush, M.F. / Pagano, M. / Zheng, N. | ||||||
Citation | Journal: Nature / Year: 2013 Title: SCFFBXL3 ubiquitin ligase targets cryptochromes at their cofactor pocket. Authors: Xing, W. / Busino, L. / Hinds, T.R. / Marionni, S.T. / Saifee, N.H. / Bush, M.F. / Pagano, M. / Zheng, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i6e.cif.gz | 209.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i6e.ent.gz | 170.6 KB | Display | PDB format |
PDBx/mmJSON format | 4i6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4i6e_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
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Full document | 4i6e_full_validation.pdf.gz | 442.8 KB | Display | |
Data in XML | 4i6e_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 4i6e_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/4i6e ftp://data.pdbj.org/pub/pdb/validation_reports/i6/4i6e | HTTPS FTP |
-Related structure data
Related structure data | 4i6gC 4i6jC 3cvuS C: citing same article (ref.) 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: 58689.047 Da / Num. of mol.: 1 / Fragment: UNP residues 1-512 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES-imadzole, pH6.5, 7.2% PEG8000, 20% Ethylene glycol (v/v), 0.03M NaF,NaBr,NaI, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2011 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 16379 / Num. obs: 16379 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 45.023 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 7.579 / Num. unique all: 815 / Rsym value: 0.191 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CVU Resolution: 2.7→48.744 Å / SU ML: 0.42 / σ(F): 0 / Phase error: 32.72 / Stereochemistry target values: MLHL
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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: 2.7→48.744 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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