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- PDB-4q5y: Crystal structure of extended-Tudor 10-11 of Drosophila melanogaster -
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Open data
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Basic information
Entry | Database: PDB / ID: 4q5y | ||||||
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Title | Crystal structure of extended-Tudor 10-11 of Drosophila melanogaster | ||||||
![]() | Maternal protein tudor | ||||||
![]() | TRANSCRIPTION / tudor domain / recognize sDMA of Aubergine / sDMA of Aubergine / nucleus | ||||||
Function / homology | ![]() pole cell development / positive regulation of post-transcriptional gene silencing by RNA / P granule assembly / methylation-dependent protein binding / pole plasm / secondary piRNA processing / pole plasm assembly / P granule organization / pole cell formation / piRNA processing ...pole cell development / positive regulation of post-transcriptional gene silencing by RNA / P granule assembly / methylation-dependent protein binding / pole plasm / secondary piRNA processing / pole plasm assembly / P granule organization / pole cell formation / piRNA processing / intracellular mRNA localization / P granule / oogenesis / germ cell development / spermatogenesis / mitochondrion / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, H. / Ren, R. / Wang, W. / Wang, M. / Yang, N. / Dong, Y. / Gong, W. / Lehmann, R. / Xu, R.M. | ||||||
![]() | ![]() Title: Structure and domain organization of Drosophila Tudor Authors: Ren, R. / Liu, H. / Wang, W. / Wang, M. / Yang, N. / Dong, Y.H. / Gong, W. / Lehmann, R. / Xu, R.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.6 KB | Display | ![]() |
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PDB format | ![]() | 60.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.4 KB | Display | ![]() |
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Full document | ![]() | 444.3 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4q5wC ![]() 3ntkS C: citing same article ( S: Starting model for refinement |
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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: 40323.484 Da / Num. of mol.: 1 / Fragment: extended-Tudor 10-11, UNP residues 2164-2515 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: 4.2 Å3/Da / Density % sol: 70.74 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 60% Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 10, 2009 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99985 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 13994 / Num. obs: 13606 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 1.9 / Num. unique all: 536 / % possible all: 79.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NTK Resolution: 3→50 Å / σ(F): 0 / Stereochemistry target values: ML
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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