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Open data
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Basic information
Entry | Database: PDB / ID: 4p1z | ||||||
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Title | Structure of the MID domain from MIWI | ||||||
![]() | Piwi-like protein 1 | ||||||
![]() | RNA BINDING PROTEIN / MID domain / MIWI / piRNA biogenesis | ||||||
Function / homology | ![]() primary piRNA processing / mRNA cap binding complex binding / piRNA-mediated retrotransposon silencing by heterochromatin formation / regulation of cytoplasmic translation / piRNA binding / piRNA processing / sperm DNA condensation / chromatoid body / dense body / regulatory ncRNA-mediated gene silencing ...primary piRNA processing / mRNA cap binding complex binding / piRNA-mediated retrotransposon silencing by heterochromatin formation / regulation of cytoplasmic translation / piRNA binding / piRNA processing / sperm DNA condensation / chromatoid body / dense body / regulatory ncRNA-mediated gene silencing / P granule / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / spermatid development / RNA endonuclease activity / meiotic cell cycle / spermatogenesis / single-stranded RNA binding / mRNA binding / protein kinase binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cora, E. / McCarthy, A.A. / Pillai, R.S. | ||||||
![]() | ![]() Title: The MID-PIWI module of Piwi proteins specifies nucleotide- and strand-biases of piRNAs. Authors: Cora, E. / Pandey, R.R. / Xiol, J. / Taylor, J. / Sachidanandam, R. / McCarthy, A.A. / Pillai, R.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 206 KB | Display | ![]() |
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PDB format | ![]() | 169.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.4 KB | Display | ![]() |
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Full document | ![]() | 451.3 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Refine code: 3
NCS oper:
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Components
#1: Protein | Mass: 14400.985 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.73 % / Description: Plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 26-32% PEG 4000, 100mM Tris-HCl, 100-200mM MgCl2 / PH range: 7.8-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 24331 / % possible obs: 98.8 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.3→2.5 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.3 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 177.11 Å2 / Biso mean: 79.951 Å2 / Biso min: 46.32 Å2
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Refinement step | Cycle: final / Resolution: 2.3→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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