+Open data
-Basic information
Entry | Database: PDB / ID: 4p1z | ||||||
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Title | Structure of the MID domain from MIWI | ||||||
Components | Piwi-like protein 1 | ||||||
Keywords | RNA BINDING PROTEIN / MID domain / MIWI / piRNA biogenesis | ||||||
Function / homology | Function and homology information primary piRNA processing / mRNA cap binding complex binding / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / : / sperm DNA condensation / chromatoid body / dense body / P granule / regulatory ncRNA-mediated gene silencing ...primary piRNA processing / mRNA cap binding complex binding / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / : / sperm DNA condensation / chromatoid body / dense body / P granule / regulatory ncRNA-mediated gene silencing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / spermatid development / RNA endonuclease activity / meiotic cell cycle / regulation of translation / spermatogenesis / single-stranded RNA binding / mRNA binding / protein kinase binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Cora, E. / McCarthy, A.A. / Pillai, R.S. | ||||||
Citation | Journal: Rna / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p1z.cif.gz | 206 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p1z.ent.gz | 169.7 KB | Display | PDB format |
PDBx/mmJSON format | 4p1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/4p1z ftp://data.pdbj.org/pub/pdb/validation_reports/p1/4p1z | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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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.) Mus musculus (house mouse) / Gene: Piwil1, Miwi / Plasmid: pProExHtb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): Rosetta / References: UniProt: Q9JMB7 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 34.58 / SU ML: 0.341 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.41 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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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