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- PDB-6mrk: Crystal structure of dmNxf2 NTF2-like domain in complex with Nxt1/p15 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mrk | |||||||||
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Title | Crystal structure of dmNxf2 NTF2-like domain in complex with Nxt1/p15 | |||||||||
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![]() | RNA BINDING PROTEIN / Piwi / transposon silencing / heterochromatin formation / piRNA pathway / transcriptional silencing | |||||||||
Function / homology | ![]() Transport of Mature mRNA derived from an Intron-Containing Transcript / piRNA-mediated retrotransposon silencing by heterochromatin formation / nuclear pore central transport channel / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / negative regulation of innate immune response / transcription repressor complex / protein import into nucleus / nuclear envelope / defense response to Gram-negative bacterium ...Transport of Mature mRNA derived from an Intron-Containing Transcript / piRNA-mediated retrotransposon silencing by heterochromatin formation / nuclear pore central transport channel / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / negative regulation of innate immune response / transcription repressor complex / protein import into nucleus / nuclear envelope / defense response to Gram-negative bacterium / single-stranded RNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wang, J. / Patel, D.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation. Authors: Batki, J. / Schnabl, J. / Wang, J. / Handler, D. / Andreev, V.I. / Stieger, C.E. / Novatchkova, M. / Lampersberger, L. / Kauneckaite, K. / Xie, W. / Mechtler, K. / Patel, D.J. / Brennecke, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.8 KB | Display | ![]() |
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PDB format | ![]() | 107.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6opfC ![]() 1jkgS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23645.662 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 15195.997 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source 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: 2.4 Å3/Da / Density % sol: 48.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 1.6 M magnesium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→77.9 Å / Num. obs: 19083 / % possible obs: 99.9 % / Redundancy: 5.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.412 / Num. unique obs: 2732 / CC1/2: 0.904 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JKG Resolution: 2.8→66.91 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.889 / SU B: 15.672 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.085 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→66.91 Å
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Refine LS restraints |
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