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Open data
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Basic information
Entry | Database: PDB / ID: 8gci | ||||||
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Title | Crystal structure of C. elegans LIN-42 PAS-B domain | ||||||
![]() | Period protein homolog lin-42 | ||||||
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Function / homology | ![]() negative regulation of dauer larval development / regulation of development, heterochronic / entrainment of circadian clock by photoperiod / transcription corepressor binding / negative regulation of miRNA transcription / circadian regulation of gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Spangler, B.K. / Coronado, A.R. / Tripathi, S.M. / Ward, J.D. / Partch, C.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of C. elegans LIN-42 PAS-B domain Authors: Spangler, B.K. / Coronado, A.R. / Tripathi, S.M. / Ward, J.D. / Partch, C.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50 KB | Display | ![]() |
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PDB format | ![]() | 32.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3gecS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31185.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.66 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.15M Lithium sulfate, 1.5M sodium potassium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.42→45.94 Å / Num. obs: 16123 / % possible obs: 99.52 % / Redundancy: 7.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.42→2.51 Å / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1634 / CC1/2: 0.895 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3GEC Resolution: 2.42→45.94 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 28.88 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→45.94 Å
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Refine LS restraints |
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LS refinement shell |
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