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- PDB-5fis: Exonuclease domain-containing 1 (Exd1) in the Gd bound conformation -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fis | ||||||
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Title | Exonuclease domain-containing 1 (Exd1) in the Gd bound conformation | ||||||
![]() | (EXD1) x 2 | ||||||
![]() | HYDROLASE / EXONUCLEASE / PIRNA BIOGENESIS / DIMER / RNA BINDING | ||||||
Function / homology | ![]() PET complex / piRNA processing / regulatory ncRNA-mediated gene silencing / P granule / meiotic cell cycle / protein homodimerization activity / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, Z. / Chen, K.M. / Pandey, R.R. / Homolka, D. / Reuter, M. / Rodino Janeiro, B.K. / Sachidanandam, R. / Fauvarque, M.O. / McCarthy, A.A. / Pillai, R.S. | ||||||
![]() | ![]() Title: Piwi Slicing and Exd1 Drive Biogenesis of Nuclear Pirnas from Cytosolic Targets of the Mouse Pirna Pathway Authors: Yang, Z. / Chen, K.M. / Pandey, R.R. / Homolka, D. / Reuter, M. / Rodino Janeiro, B.K. / Sachidanandam, R. / Fauvarque, M.O. / 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 | ![]() | 172.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.8 KB | Display | ![]() |
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Full document | ![]() | 440.6 KB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 35.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.99816, -0.00371, -0.06055), Vector: |
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Components
#1: Protein | Mass: 28118.447 Da / Num. of mol.: 1 / Fragment: EXONUCLEASE DOMAIN, RESIDUES 73-315 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 28146.463 Da / Num. of mol.: 1 / Fragment: EXONUCLEASE DOMAIN, RESIDUES 73-315 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | PROTEIN SEQUENCE CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.4 % / Description: OSCILLATION DATA WERE COLLECTED USING MXCUBEV2 |
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Crystal grow | pH: 6 Details: 10% (W/V) PEG 2K, 200 MM KCL, 50 MM NA CACODYLATE (PH=6) 2 MM GDCL3, |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2013 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 143744 / % possible obs: 97.2 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.6→1.65 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.9 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.6→50.01 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.257 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.586 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50.01 Å
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Refine LS restraints |
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