+Open data
-Basic information
Entry | Database: PDB / ID: 5f6a | ||||||
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Title | Drosophila Melanogaster Cycle W398A PAS-B with Empty Pocket | ||||||
Components | Protein cycle | ||||||
Keywords | CIRCADIAN CLOCK PROTEIN / PAS / Glycerol / 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 / locomotor rhythm / behavioral response to cocaine / 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: 1.93 Å | ||||||
Authors | Manahan, C.C. / Crane, B.R. | ||||||
Citation | Journal: To Be Published Title: Drosophila Melanogaster Cycle PAS-B 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 | 5f6a.cif.gz | 57.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f6a.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 5f6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/5f6a ftp://data.pdbj.org/pub/pdb/validation_reports/f6/5f6a | 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: 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: 2.32 Å3/Da / Density % sol: 46.9 % |
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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: F1 / Wavelength: 0.987 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 R 100K-A / Detector: PIXEL / Date: Nov 5, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.93→50 Å / Num. obs: 6663 / % possible obs: 78.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 26.38 Å2 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.064 / Rrim(I) all: 0.117 / Χ2: 0.962 / Net I/av σ(I): 9.476 / Net I/σ(I): 4.3 / Num. measured all: 19318 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Resolution: 1.93→34.516 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.91 / 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: 76.33 Å2 / Biso mean: 32.6755 Å2 / Biso min: 17.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.93→34.516 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: 5
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Refinement TLS params. | Method: refined / Origin x: 136.4226 Å / Origin y: 3.8188 Å / Origin z: 51.211 Å
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Refinement TLS group |
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