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- PDB-5xyv: Crystal structure of drosophila melanogaster Rhino chromoshadow d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xyv | ||||||
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Title | Crystal structure of drosophila melanogaster Rhino chromoshadow domain in complex with Deadlock N-terminal domain | ||||||
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![]() | PROTEIN BINDING / piRNA pathway / Chromoshadow / Complex | ||||||
Function / homology | ![]() piRNA transcription / positive regulation of piRNA transcription / Rhino-Deadlock-Cutoff Complex / oocyte localization involved in germarium-derived egg chamber formation / germarium-derived egg chamber formation / fusome organization / positive regulation of snRNA transcription by RNA polymerase II / chorion-containing eggshell pattern formation / oocyte karyosome formation / piRNA processing ...piRNA transcription / positive regulation of piRNA transcription / Rhino-Deadlock-Cutoff Complex / oocyte localization involved in germarium-derived egg chamber formation / germarium-derived egg chamber formation / fusome organization / positive regulation of snRNA transcription by RNA polymerase II / chorion-containing eggshell pattern formation / oocyte karyosome formation / piRNA processing / oocyte development / oogenesis / chromosome organization / heterochromatin / pericentric heterochromatin / : / mitotic spindle organization / transcription antitermination / heterochromatin formation / chromosome / centrosome / chromatin binding / chromatin / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yu, B.W. / Huang, Y. | ||||||
![]() | ![]() Title: Structural insights into Rhino-Deadlock complex for germline piRNA cluster specification Authors: Yu, B. / Lin, Y.A. / Parhad, S.S. / Jin, Z. / Ma, J. / Theurkauf, W.E. / Zhang, Z.Z. / Huang, Y. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.4 KB | Display | ![]() |
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PDB format | ![]() | 44.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5xywC ![]() 2fmmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8577.806 Da / Num. of mol.: 2 / Fragment: UNP residues 353-418 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 7107.214 Da / Num. of mol.: 2 / Fragment: UNP residues 1-60 Source method: isolated from a genetically manipulated source Details: In the electron density maps we only observed the main chain of 45R, so we used Alanine instead. Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.95 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25%(W/V) PEG3350, 0.1 M HEPES (pH 7.5), 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 16741 / % possible obs: 99.4 % / Redundancy: 8.1 % / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 16741 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FMM Resolution: 2.1→29.651 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 24.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→29.651 Å
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Refine LS restraints |
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LS refinement shell |
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