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Yorodumi- PDB-4q5y: Crystal structure of extended-Tudor 10-11 of Drosophila melanogaster -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q5y | ||||||
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Title | Crystal structure of extended-Tudor 10-11 of Drosophila melanogaster | ||||||
Components | Maternal protein tudorMother | ||||||
Keywords | TRANSCRIPTION / tudor domain / recognize sDMA of Aubergine / sDMA of Aubergine / nucleus | ||||||
Function / homology | Function and homology information pole cell development / positive regulation of post-transcriptional gene silencing by RNA / P granule assembly / methylation-dependent protein binding / pole plasm / secondary piRNA processing / P granule organization / pole plasm assembly / 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 / P granule organization / pole plasm assembly / pole cell formation / piRNA processing / intracellular mRNA localization / P granule / oogenesis / germ cell development / spermatogenesis / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Liu, H. / Ren, R. / Wang, W. / Wang, M. / Yang, N. / Dong, Y. / Gong, W. / Lehmann, R. / Xu, R.M. | ||||||
Citation | Journal: Cell Res. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q5y.cif.gz | 82.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q5y.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 4q5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/4q5y ftp://data.pdbj.org/pub/pdb/validation_reports/q5/4q5y | HTTPS FTP |
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-Related structure data
Related structure data | 4q5wC 3ntkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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.) Drosophila melanogaster (fruit fly) / Gene: CG9450, tud, tudor / Plasmid: pET28-smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: P25823 |
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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: 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: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99985 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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