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Yorodumi- PDB-6qv4: Crystal structure of the Ski2 RNA-helicase Brr2 from Chaetomium t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qv4 | ||||||
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Title | Crystal structure of the Ski2 RNA-helicase Brr2 from Chaetomium thermophilum bound to ATP-gamma-S | ||||||
Components | Pre-mRNA splicing helicase-like protein | ||||||
Keywords | RNA BINDING PROTEIN / Helicase ATP-gamma-S Brr2 Ski2 Chaetomium thermophilum splicing RNA | ||||||
Function / homology | Function and homology information helicase activity / mRNA processing / nucleic acid binding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Absmeier, E. / Santos, K.F. / Wahl, M.C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Structure / Year: 2020 Title: Molecular Mechanism Underlying Inhibition of Intrinsic ATPase Activity in a Ski2-like RNA Helicase. Authors: Absmeier, E. / Santos, K.F. / Wahl, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qv4.cif.gz | 702.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qv4.ent.gz | 573.9 KB | Display | PDB format |
PDBx/mmJSON format | 6qv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/6qv4 ftp://data.pdbj.org/pub/pdb/validation_reports/qv/6qv4 | HTTPS FTP |
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-Related structure data
Related structure data | 6qv3C 6qwsC 5m59S 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: 196442.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0009470 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0S0B9 | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.91 Å3/Da / Density % sol: 57.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: Tris-HCl, Peg8000, calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.8814 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.8814 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 625210 / Num. obs: 60260 / % possible obs: 98.9 % / Redundancy: 10.4 % / CC1/2: 0.999 / Rrim(I) all: 0.151 / Net I/σ(I): 10.19 |
Reflection shell | Resolution: 2.7→2.86 Å / Redundancy: 10.3 % / Num. unique all: 4413 / Num. unique obs: 45316 / CC1/2: 0.387 / Rrim(I) all: 2.516 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M59 Resolution: 2.8→44.526 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 29.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→44.526 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -100.1255 Å / Origin y: 185.2778 Å / Origin z: -16.2658 Å
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Refinement TLS group | Selection details: all |