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- PDB-6f3h: Crystal structure of Dss1 exoribonuclease active site mutant D477... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6f3h | ||||||
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Title | Crystal structure of Dss1 exoribonuclease active site mutant D477N from Candida glabrata | ||||||
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![]() | HYDROLASE / 3' to 5' exoribonuclease RNA degradation mitochondria | ||||||
Function / homology | ![]() mitochondrial degradosome / mitochondrial RNA catabolic process / exoribonuclease II activity / RNA nuclease activity / mitochondrion / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Razew, M. / Nowak, E. / Nowotny, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components. Authors: Razew, M. / Warkocki, Z. / Taube, M. / Kolondra, A. / Czarnocki-Cieciura, M. / Nowak, E. / Labedzka-Dmoch, K. / Kawinska, A. / Piatkowski, J. / Golik, P. / Kozak, M. / Dziembowski, A. / Nowotny, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 619.1 KB | Display | ![]() |
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PDB format | ![]() | 520.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.3 KB | Display | ![]() |
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Full document | ![]() | 488.1 KB | Display | |
Data in XML | ![]() | 55.8 KB | Display | |
Data in CIF | ![]() | 78.2 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 95343.742 Da / Num. of mol.: 2 / Mutation: D477N Source method: isolated from a genetically manipulated source Details: 69 N-terminal truncation was introduced in the full length protein Source: (gene. exp.) ![]() Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65 Gene: CAGL0M07051g / Production host: ![]() ![]() #2: RNA chain | | Mass: 1899.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RNA molecule co-purified with the protein / Source: (natural) ![]() ![]() #3: RNA chain | | Mass: 1875.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RNA molecule co-purified with the protein / Source: (natural) ![]() ![]() #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.25 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES monohydrate (pH 6.5) and 6% (w/v) PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→29.211 Å / Num. obs: 129398 / % possible obs: 98.8 % / Redundancy: 4.6 % / Rrim(I) all: 0.173 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.7→2.77 Å / Rrim(I) all: 0.938 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 2.703→29.211 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: -10.7182 Å / Origin y: 60.2468 Å / Origin z: 40.2839 Å
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Refinement TLS group | Selection details: all |