+Open data
-Basic information
Entry | Database: PDB / ID: 7jw2 | ||||||
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Title | Crystal structure of Aedes aegypti Nibbler EXO domain | ||||||
Components | Exonuclease mut-7 homolog | ||||||
Keywords | RNA BINDING PROTEIN / Nibbler / exoribonuclease / microRNA trimming / piRNA trimming | ||||||
Function / homology | Function and homology information 3'-5' exonuclease activity / nucleic acid binding / Hydrolases; Acting on ester bonds / metal ion binding Similarity search - Function | ||||||
Biological species | Aedes aegypti (yellow fever mosquito) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Xie, W. / Sowemimo, I. / Hayashi, R. / Wang, J. / Brennecke, J. / Ameres, S.L. / Patel, D.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Structure-function analysis of microRNA 3'-end trimming by Nibbler. Authors: Xie, W. / Sowemimo, I. / Hayashi, R. / Wang, J. / Burkard, T.R. / Brennecke, J. / Ameres, S.L. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jw2.cif.gz | 133.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jw2.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 7jw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jw2_validation.pdf.gz | 433.1 KB | Display | wwPDB validaton report |
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Full document | 7jw2_full_validation.pdf.gz | 437.5 KB | Display | |
Data in XML | 7jw2_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 7jw2_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/7jw2 ftp://data.pdbj.org/pub/pdb/validation_reports/jw/7jw2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26129.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: AAEL005527 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q179T2, Hydrolases; Acting on ester bonds #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: 46.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium formate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→37.28 Å / Num. obs: 72680 / % possible obs: 98.85 % / Redundancy: 4.5 % / Biso Wilson estimate: 18.39 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.03341 / Rpim(I) all: 0.01727 / Rrim(I) all: 0.03775 / Net I/σ(I): 26.22 |
Reflection shell | Resolution: 1.5→1.554 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.1528 / Mean I/σ(I) obs: 5.74 / Num. unique obs: 6711 / CC1/2: 0.983 / CC star: 0.996 / Rpim(I) all: 0.09235 / Rrim(I) all: 0.1796 / % possible all: 91.92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Drosophila Nbr EXO domain Resolution: 1.5→37.28 Å / SU ML: 0.1501 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.9256 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→37.28 Å
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Refine LS restraints |
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LS refinement shell |
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