+Open data
-Basic information
Entry | Database: PDB / ID: 7dey | ||||||
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Title | Structure of Dicer from Pichia stipitis | ||||||
Components | RNase IIIRibonuclease III | ||||||
Keywords | SPLICING / RNase III | ||||||
Function / homology | Function and homology information rRNA catabolic process / ribonuclease III activity / rRNA processing / double-stranded RNA binding Similarity search - Function | ||||||
Biological species | Scheffersomyces stipitis (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.897 Å | ||||||
Authors | Jobichen, C. / Jingru, C. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: Protein Sci. / Year: 2021 Title: Structural and mechanistic insight into stem-loop RNA processing by yeast Pichia stipitis Dicer. Authors: Chan, J. / Qinqin, F. / Jianwei, L. / Ying, C. / Machida, S. / Wei, C. / Yuan, Y.A. / Jobichen, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dey.cif.gz | 167.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dey.ent.gz | 130.7 KB | Display | PDB format |
PDBx/mmJSON format | 7dey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/7dey ftp://data.pdbj.org/pub/pdb/validation_reports/de/7dey | HTTPS FTP |
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-Related structure data
Related structure data | 4oogS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26323.910 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (fungus) Strain: ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545 / Gene: PICST_30953 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3LS79 |
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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: 4.01 Å3/Da / Density % sol: 73.69 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / Details: 3.6 M NaCl and 0.1 M sodium acetate (pH 5.4-5.6) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.987 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.897→50 Å / Num. obs: 37041 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 79.79 Å2 / Rsym value: 0.21 / Net I/σ(I): 20.52 |
Reflection shell | Resolution: 2.9→2.95 Å / Num. unique obs: 1824 / Rsym value: 0.94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OOG Resolution: 2.897→29.682 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.897→29.682 Å
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Refine LS restraints |
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LS refinement shell |
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