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Yorodumi- PDB-6d2z: Structure of human Usb1 with uridine-adenosine, inactive H208Q mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d2z | |||||||||
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Title | Structure of human Usb1 with uridine-adenosine, inactive H208Q mutant | |||||||||
Components |
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Keywords | HYDROLASE/RNA / exonuclease / U6 snRNA / 2H phosphodiesterase superfamily / HYDROLASE / HYDROLASE-RNA complex | |||||||||
Function / homology | Function and homology information poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends / U6 snRNA 3'-end processing / snRNA 3'-end processing / intercellular bridge / RNA splicing / Lyases; Phosphorus-oxygen lyases / 3'-5'-RNA exonuclease activity / lyase activity / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å | |||||||||
Authors | Nomura, Y. / Montemayor, E.J. / Butcher, S.E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1. Authors: Nomura, Y. / Roston, D. / Montemayor, E.J. / Cui, Q. / Butcher, S.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d2z.cif.gz | 130.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d2z.ent.gz | 100.1 KB | Display | PDB format |
PDBx/mmJSON format | 6d2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/6d2z ftp://data.pdbj.org/pub/pdb/validation_reports/d2/6d2z | HTTPS FTP |
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-Related structure data
Related structure data | 6d30C 6d31C 5v1mS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 22176.482 Da / Num. of mol.: 1 / Mutation: H208Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USB1, C16orf57 / Production host: Escherichia coli (E. coli) References: UniProt: Q9BQ65, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
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#2: RNA chain | Mass: 590.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.21 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 100 mM bis-tris, 25% SOKALAN CP 42, 1.5% tetrahydrofuran |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 13, 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: 1.18→44.53 Å / Num. obs: 55920 / % possible obs: 91.6 % / Redundancy: 6.6 % / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.18→1.2 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5V1M Resolution: 1.18→44.53 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 18.94
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→44.53 Å
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Refine LS restraints |
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LS refinement shell |
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