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Yorodumi- PDB-5f68: Drosophila Melanogaster Cycle W398A PAS-B with Bound Ethylene Glycol -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f68 | ||||||
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Title | Drosophila Melanogaster Cycle W398A PAS-B with Bound Ethylene Glycol | ||||||
Components | Protein cycle | ||||||
Keywords | CIRCADIAN CLOCK PROTEIN / PAS / Ethylene Glycol / Clock / BMAL | ||||||
Function / homology | Function and homology information Transcription regulation of cwo gene / Transcription activation by CLK:CYC and repression by VRI / NPAS4 regulates expression of target genes / circadian regulation of heart rate / Circadian Clock pathway / eclosion rhythm / Transcription repression by PER and activation by PDP1 / Dephosphorylation of PER / Degradation of PER / Degradation of TIM ...Transcription regulation of cwo gene / Transcription activation by CLK:CYC and repression by VRI / NPAS4 regulates expression of target genes / circadian regulation of heart rate / Circadian Clock pathway / eclosion rhythm / Transcription repression by PER and activation by PDP1 / Dephosphorylation of PER / Degradation of PER / Degradation of TIM / rhythmic behavior / regulation of circadian sleep/wake cycle, sleep / aryl hydrocarbon receptor complex / response to starvation / behavioral response to cocaine / locomotor rhythm / circadian regulation of gene expression / circadian rhythm / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.23 Å | ||||||
Authors | Manahan, C.C. / Crane, B.R. | ||||||
Citation | Journal: To Be Published Title: Drosophila Melanogaster Cycle PAS-B with Bound Ethylene Glycol Authors: Manahan, C.C. / 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 | 5f68.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f68.ent.gz | 40.5 KB | Display | PDB format |
PDBx/mmJSON format | 5f68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/5f68 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/5f68 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 12106.827 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cyc, CG8727 / Production host: Escherichia coli (E. coli) / References: UniProt: O61734 |
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#2: Chemical | ChemComp-EDO / |
#3: 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: 2.33 Å3/Da / Density % sol: 47.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.987 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 14, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.23→50 Å / Num. obs: 30239 / % possible obs: 93.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.066 / Rrim(I) all: 0.121 / Χ2: 3.029 / Net I/av σ(I): 12.084 / Net I/σ(I): 5 / Num. measured all: 95323 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Resolution: 1.23→34.915 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.13 / Stereochemistry target values: ML
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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 max: 49.69 Å2 / Biso mean: 14.5717 Å2 / Biso min: 5.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.23→34.915 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: 80.4771 Å / Origin y: 17.9789 Å / Origin z: 16.7144 Å
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Refinement TLS group |
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